arXiv subjects

I. Vattulainen

Publications and source records attributed to I. Vattulainen.

16 recordsLinked to original sources

arXiv2005

Reptational dynamics in dissipative particle dynamics simulations of polymer melts

Understanding the complex viscoelastic properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for the topological constraints in polymeric liquids using the Dissipative Particle Dynamics (DPD). The same approach is also applicable in other soft potential models. For short chains the model correctly reproduces Rouse-like dynamics whereas for longer chains the dynamics becomes reptational as the chain length is increased - something that is not attainable using standard DPD or other coarse-grained soft potential methods. Importantly, no new length scales or forces need to be added.

cond-mat.soft↗

arXiv2005

Dielectrophoresis of nanocolloids: a molecular dynamics study

Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for polarizable nanoparticles, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature.

cond-mat.soft↗

arXiv2003

On coarse-graining by the Inverse Monte Carlo method: Dissipative Particle Dynamics simulations made to a precise tool in soft matter modeling

We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD) simulations, which are then used in coarse-grained dissipative particle dynamics (DPD) simulations. Here, the effective potentials were obtained by applying the Inverse Monte Carlo method [Lyubartsev and Laaksonen, Phys. Rev. E. vol. 52, 3730 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. In our first application of the method, the effective potentials were used in DPD simulations of aqueous NaCl solutions. With the same computational effort we were able to simulate systems of one order of magnitude larger as compared to the MD simulations. The results from the MD and DPD simulations are found to be in excellent agreement.

cond-mat.soft↗

arXiv2003

How would you integrate the equations of motion in dissipative particle dynamics simulations?

In this work we assess the quality and performance of several novel dissipative particle dynamics integration schemes that have not previously been tested independently. Based on a thorough comparison we identify the respective methods of Lowe and Shardlow as particularly promising candidates for future studies of large-scale properties of soft matter systems.

cond-mat.soft↗

arXiv2003

Influence of hydrodynamics on many-particle diffusion in 2D colloidal suspensions

We study many-particle diffusion in 2D colloidal suspensions with full hydrodynamic interactions through a novel mesoscopic simulation technique. We focus on the behaviour of the effective scaled tracer and collective diffusion coefficients $D_T(ρ) / D_0$ and $D_C(ρ) / D_0$, where $D_0$ is the single-particle diffusion coefficient, as a function of the density of the colloids $ρ$. At low Schmidt numbers $Sc={\cal O}(1)$, we find that hydrodynamics has essentially no effect on the behaviour of $D_T(ρ)/D_0$. At larger $Sc$, $D_T(ρ)/D_0$ is enhanced at all densities, although the differences compared to the case without hydrodynamics are minor. The collective diffusion coefficient, on the other hand, is much more strongly coupled to hydrodynamical conservation laws and is distinctly different from the purely dissipative case.

cond-mat.soft↗

arXiv2003

Dynamics and Scaling of 2D Polymers in a Dilute Solution

The breakdown of dynamical scaling for a dilute polymer solution in 2D has been suggested by Shannon and Choy [Phys. Rev. Lett. {\bf 79}, 1455 (1997)]. However, we show here both numerically and analytically that dynamical scaling holds when the finite-size dependence of the relevant dynamical quantities is properly taken into account. We carry out large-scale simulations in 2D for a polymer chain in a good solvent with full hydrodynamic interactions to verify dynamical scaling. This is achieved by novel mesoscopic simulation techniques.

cond-mat.soft↗

arXiv2002

Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts due to Truncating Electrostatic Interactions

We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using the Particle-Mesh Ewald (PME) technique. All examined truncation distances (1.8 to 2.5 nm) lead to major effects on the bilayer properties, such as enhanced order of acyl chains together with decreased areas per lipid. The results obtained using PME, on the other hand, are consistent with experiments. These artifacts are interpreted in terms of radial distribution functions $g(r)$ of molecules and molecular groups in the bilayer plane. Pronounced maxima or minima in g(r) appear exactly at the cutoff distance indicating that the truncation gives rise to artificial ordering between the polar phosphatidyl and choline groups of the DPPC molecules. In systems described using PME, such artificial ordering is not present.

cond-mat.soft↗

arXiv1997

Non-Arrhenius Behavior of Surface Diffusion Near a Phase Transition Boundary

We study the non-Arrhenius behavior of surface diffusion near the second-order phase transition boundary of an adsorbate layer. In contrast to expectations based on macroscopic thermodynamic effects, we show that this behavior can be related to the average microscopic jump rate which in turn is determined by the waiting-time distribution W(t) of single-particle jumps at short times. At long times, W(t) yields a barrier that corresponds to the rate-limiting step in diffusion. The microscopic information in W(t) should be accessible by STM measurements.

cond-mat.soft↗

arXiv1997

A Dynamical Mean Field Theory for the Study of Surface Diffusion Constants

We present a combined analytical and numerical approach based on the Mori projection operator formalism and Monte Carlo simulations to study surface diffusion within the lattice-gas model. In the present theory, the average jump rate and the susceptibility factor appearing are evaluated through Monte Carlo simulations, while the memory functions are approximated by the known results for a Langmuir gas model. This leads to a dynamical mean field theory (DMF) for collective diffusion, while approximate correlation effects beyond DMF are included for tracer diffusion. We apply our formalism to three very different strongly interacting systems and compare the results of the new approach with those of usual Monte Carlo simulations. We find that the combined approach works very well for collective diffusion, whereas for tracer diffusion the influence of interactions on the memory effects is more prominent.

cond-mat.soft↗

arXiv1996

Non-equilibrium surface diffusion in the O/W(110) system

In this Letter, we present results of an extensive Monte Carlo study of the O/W(110) system under non-equilibrium conditions. We study the mean square displacements and long wavelength density fluctuations of adatoms. From these quantities, we define effective and time-dependent values for the collective and tracer diffusion mobilities. These mobilities reduce to the usual diffusion constants when equilibrium is reached. We discuss our results in view of existing experimental measurements of effective diffusion barriers, and the difficulties associated with interpreting non-equilibrium data.

cond-mat↗

arXiv1994

New tests of random numbers for simulations in physical systems

The aim of this Thesis is to present five new tests for random numbers, which are widely used {\em e.g.} in computer simulations in physics applications. The first two tests, the cluster test and the autocorrelation test, are based on analogies to the two-dimensional Ising model. The next two, the random walk test and the $n$-block test, are based on studies of random walks, and the condition number test presented last uses some results of Gaussian distributed random matrices. Studies with several commonly used pseudorandom number generators reveal that the cluster test is particularly powerful in finding periodic correlations on bit level, and that the autocorrelation test, the random walk test, and the $n$-block test are very effective in detecting short-ranged correlations. The results of the condition number test are mostly inconclusive, however. By means of the tests presented in this work, two important results are found. First, we show quantitatively that the reason for erroneous results in some recent high precision Monte Carlo simulations for some commonly used pseudorandom number generators are the so called triple correlations in the sequences. Then, we show that the properties of such a sequence may be considerably improved, if only a certain portion of it is used.

cond-mat↗

arXiv1994

Physical tests for Random Numbers in Simulations

We propose three physical tests to measure correlations in random numbers used in Monte Carlo simulations. The first test uses autocorrelation times of certain physical quantities when the Ising model is simulated with the Wolff algorithm. The second test is based on random walks, and the third on blocks of n successive numbers. We apply the tests to show that recent errors in high precision simulations using generalized feedback shift register algorithms are due to short range correlations in random number sequences. We also determine the length of these correlations.

cond-mat↗

arXiv1993

Bit Level Correlations in Some Pseudorandom Number Generators

We present results of extensive bit level tests on some pseudorandom number generators which are commonly used in physics applications. The generators have first been tested with an extended version of the $d$-tuple test. Second, we have developed a novel {\it cluster test} where a physical analogy of the binary numbers with the two dimensional Ising model has been utilized. We demonstrate that the new test is rather powerful in finding periodic correlations on bit level. Results of both test methods are presented for each bit of the output of the generators. Some generators exhibit clear bit level correlations but we find no evidence of discernible correlations for generators, which have recently produced systematic errors in Monte Carlo simulations.

hep-lat↗

arXiv1993

Influence of Implementation on the Properties of Pseudorandom Number Generators with a Carry Bit

We present results of extensive statistical and bit level tests on three implementations of a pseudorandom number generator algorithm using the lagged Fibonacci method with an occasional addition of an extra bit. First implementation is the RCARRY generator of James, which uses subtraction. The second is a modified version of it, where a suggested error present in the original implementation has been corrected. The third is our modification of RCARRY such that it utilizes addition of the carry bit. Our results show that there are no significant differences between the performance of these three generators.

hep-lat↗

arXiv1993

A Comparative Study of Some Pseudorandom Number Generators

We present results of an extensive test program of a group of pseudorandom number generators which are commonly used in the applications of physics, in particular in Monte Carlo simulations. The generators include public domain programs, manufacturer installed routines and a random number sequence produced from physical noise. We start by traditional statistical tests, followed by detailed bit level and visual tests. The computational speed of various algorithms is also scrutinized. Our results allow direct comparisons between the properties of different generators, as well as an assessment of the efficiency of the various test methods. This information provides the best available criterion to choose the best possible generator for a given problem. However, in light of recent problems reported with some of these generators, we also discuss the importance of developing more refined physical tests to find possible correlations not revealed by the present test methods.

hep-lat↗

arXiv1993

Hidden Errors in Simulations and the Quality of Pseudorandom Numbers

We have carried out extensive statistical, bit level and visual tests of several random number generators used in the applications of physics. Two of the generators tested were recently included in a paper by Ferrenberg {\it et al.} (Phys. Rev. Lett. {\bf 68}, 3382 (1992)) who reported correlations in their Monte Carlo simulations. As a possible explanation of this, they suggest bit level correlations in the random numbers. However, our tests find no evidence of such correlations, which highlights the importance of more careful physical tests of random number generators.

cond-mat↗