18 research outputs found
The Complete Characterization of Fourth-Order Symplectic Integrators with Extended-Linear Coefficients
The structure of symplectic integrators up to fourth-order can be completely
and analytical understood when the factorization (split) coefficents are
related linearly but with a uniform nonlinear proportional factor. The analytic
form of these {\it extended-linear} symplectic integrators greatly simplified
proofs of their general properties and allowed easy construction of both
forward and non-forward fourth-order algorithms with arbitrary number of
operators. Most fourth-order forward integrators can now be derived
analytically from this extended-linear formulation without the use of symbolic
algebra.Comment: 12 pages, 2 figures, submitted to Phys. Rev. E, corrected typo
Accurate sampling using Langevin dynamics
We show how to derive a simple integrator for the Langevin equation and
illustrate how it is possible to check the accuracy of the obtained
distribution on the fly, using the concept of effective energy introduced in a
recent paper [J. Chem. Phys. 126, 014101 (2007)]. Our integrator leads to
correct sampling also in the difficult high-friction limit. We also show how
these ideas can be applied in practical simulations, using a Lennard-Jones
crystal as a paradigmatic case
Fourth Order Algorithms for Solving the Multivariable Langevin Equation and the Kramers Equation
We develop a fourth order simulation algorithm for solving the stochastic
Langevin equation. The method consists of identifying solvable operators in the
Fokker-Planck equation, factorizing the evolution operator for small time steps
to fourth order and implementing the factorization process numerically. A key
contribution of this work is to show how certain double commutators in the
factorization process can be simulated in practice. The method is general,
applicable to the multivariable case, and systematic, with known procedures for
doing fourth order factorizations. The fourth order convergence of the
resulting algorithm allowed very large time steps to be used. In simulating the
Brownian dynamics of 121 Yukawa particles in two dimensions, the converged
result of a first order algorithm can be obtained by using time steps 50 times
as large. To further demostrate the versatility of our method, we derive two
new classes of fourth order algorithms for solving the simpler Kramers equation
without requiring the derivative of the force. The convergence of many fourth
order algorithms for solving this equation are compared.Comment: 19 pages, 2 figure
Forward Symplectic Integrators and the Long Time Phase Error in Periodic Motions
We show that when time-reversible symplectic algorithms are used to solve
periodic motions, the energy error after one period is generally two orders
higher than that of the algorithm. By use of correctable algorithms, we show
that the phase error can also be eliminated two orders higher than that of the
integrator. The use of fourth order forward time step integrators can result in
sixth order accuracy for the phase error and eighth accuracy in the periodic
energy. We study the 1-D harmonic oscillator and the 2-D Kepler problem in
great details, and compare the effectiveness of some recent fourth order
algorithms.Comment: Submitted to Phys. Rev. E, 29 Page
On the construction of high-order force gradient algorithms for integration of motion in classical and quantum systems
A consequent approach is proposed to construct symplectic force-gradient
algorithms of arbitrarily high orders in the time step for precise integration
of motion in classical and quantum mechanics simulations. Within this approach
the basic algorithms are first derived up to the eighth order by direct
decompositions of exponential propagators and further collected using an
advanced composition scheme to obtain the algorithms of higher orders. Contrary
to the scheme by Chin and Kidwell [Phys. Rev. E 62, 8746 (2000)], where
high-order algorithms are introduced by standard iterations of a force-gradient
integrator of order four, the present method allows to reduce the total number
of expensive force and its gradient evaluations to a minimum. At the same time,
the precision of the integration increases significantly, especially with
increasing the order of the generated schemes. The algorithms are tested in
molecular dynamics and celestial mechanics simulations. It is shown, in
particular, that the efficiency of the new fourth-order-based algorithms is
better approximately in factors 5 to 1000 for orders 4 to 12, respectively. The
results corresponding to sixth- and eighth-order-based composition schemes are
also presented up to the sixteenth order. For orders 14 and 16, such highly
precise schemes, at considerably smaller computational costs, allow to reduce
unphysical deviations in the total energy up in 100 000 times with respect to
those of the standard fourth-order-based iteration approach.Comment: 23 pages, 2 figures; submitted to Phys. Rev.
Lattice Boltzmann simulations of soft matter systems
This article concerns numerical simulations of the dynamics of particles
immersed in a continuum solvent. As prototypical systems, we consider colloidal
dispersions of spherical particles and solutions of uncharged polymers. After a
brief explanation of the concept of hydrodynamic interactions, we give a
general overview over the various simulation methods that have been developed
to cope with the resulting computational problems. We then focus on the
approach we have developed, which couples a system of particles to a lattice
Boltzmann model representing the solvent degrees of freedom. The standard D3Q19
lattice Boltzmann model is derived and explained in depth, followed by a
detailed discussion of complementary methods for the coupling of solvent and
solute. Colloidal dispersions are best described in terms of extended particles
with appropriate boundary conditions at the surfaces, while particles with
internal degrees of freedom are easier to simulate as an arrangement of mass
points with frictional coupling to the solvent. In both cases, particular care
has been taken to simulate thermal fluctuations in a consistent way. The
usefulness of this methodology is illustrated by studies from our own research,
where the dynamics of colloidal and polymeric systems has been investigated in
both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures,
76 page
Dissecting the THz spectrum of liquid water from first principles via correlations in time and space
Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at ≈200 cm-1 is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 cm-1 ≈2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules—even in the absence of well-defined resonances