Search Results - "VATTULAINEN, I"

How would you integrate the equations of motion in dissipative particle dynamics simulations? by Nikunen, P, Karttunen, M, Vattulainen, I

“…In this work we assess the quality and performance of several novel dissipative particle dynamics integration schemes that have not previously been tested…”
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Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions by Patra, M., Karttunen, M., Hyvönen, M.T., Falck, E., Lindqvist, P., Vattulainen, I.

“…We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns…”
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Tracer diffusion in colloidal suspensions under dilute and crowded conditions with hydrodynamic interactions by Tomilov, A, Videcoq, A, Chartier, T, Ala-Nissilä, T, Vattulainen, I

“…We consider tracer diffusion in colloidal suspensions under solid loading conditions, where hydrodynamic interactions play an important role. To this end, we…”
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Enhanced dielectrophoresis of nanocolloids by dimer formation by Salonen, E, Terama, E, Vattulainen, I, Karttunen, M

“…We investigate the dielectrophoretic motion of charge-neutral, polarizable nanocolloids through molecular dynamics simulations. Comparison to analytical…”
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Ionic cloud distribution close to a charged surface in the presence of salt by Punkkinen, O, Naji, A, Podgornik, R, Vattulainen, I, Hansen, P.-L

“…Despite its importance, the understanding of ionic cloud distribution close to a charged macroion under physiological salt conditions has remained very limited…”
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Dielectrophoresis of nanocolloids : A molecular dynamics study by SALONEN, E, TERAMA, E, VATTULAINEN, I, KARTTUNEN, M

“…Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and…”
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Influence of hydrodynamics on many-particle diffusion in 2D colloidal suspensions by FALCK, E, LAHTINEN, J. M, VATTULAINEN, I, ALA-NISSILA, T

“…We study many-particle diffusion in 2D colloidal suspensions with full hydrodynamic interactions through a novel mesoscopic simulation technique. We focus on…”
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Memory effects in Arrhenius barriers for surface diffusion by Vattulainen, I.

“…The importance of memory effects in Arrhenius surface diffusion barriers E A is studied within the lattice-gas model. It is found that E A of tracer diffusion…”
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Effect of kinks and concerted diffusion mechanisms on mass transport and growth on stepped metal surfaces by Merikoski, J., Vattulainen, I., Heinonen, J., Ala-Nissila, T.

“…We study the effect of kinks and concerted atomic mechanisms on diffusion processes relevant to metal-on-metal homoepitaxy on fcc metal surfaces vicinal to the…”
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Physical tests for random numbers in simulations by Vattulainen, I, I, Ala-Nissila, T, Kankaala, K

“…We propose three physical tests to measure correlations in random numbers used in Monte Carlo simulations. The first test uses autocorrelation times of certain…”
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Diffusion and mobility of interacting particles on stepped surfaces by Mašı́n, M., Vattulainen, I., Ala-Nissila, T., Chvoj, Z.

“…We study the mobility and collective diffusion of mutually interacting adparticles on stepped surfaces through Monte Carlo simulations. We consider the case of…”
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Non-equilibrium effects in profile evolution measurements of surface diffusion by Nikunen, P., Vattulainen, I., Ala-Nissila, T.

“…In this work, we use the Boltzmann–Matano method to determine the collective diffusion coefficient, D C( θ), as a function of coverage, θ, from scaled coverage…”
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A comparative study of some pseudorandom number generators by Vattulainen, I., Kankaala, K., Saarinen, J., Ala-Nissila, T.

“…We present results of a test program of a group of pseudorandom number generators which are commonly used in the applications of physics, in particular in…”
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Cholesterol-dependent effect of antidepressants on activation BDNF receptor (TRKB) by Casarotto, P., Fred, S.M., Biojone, C., Girych, M., Rog, T., Vattulainen, I., Castrén, E.

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How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative by Mobarak, Edouard, Javanainen, Matti, Kulig, Waldemar, Honigmann, Alf, Sezgin, Erdinc, Aho, Noora, Eggeling, Christian, Rog, Tomasz, Vattulainen, Ilpo

“…Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced…”
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Lipid simulations: a perspective on lipids in action by Vattulainen, Ilpo, Rog, Tomasz

“…In this article, we provide an overview of lipid simulations, describing how a computer can be used as a laboratory for lipid research. We briefly discuss the…”
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A dynamical mean field theory for the study of surface diffusion constants by Hjelt, T., Vattulainen, I., Merikoski, J., Ala-Nissila, T., Ying, S.C.

“…We present a combined analytical and numerical approach based on the Mori projection operator formalism and Monte Carlo simulations to study surface diffusion…”
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Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties by Ragaller, Franziska, Andronico, Luca, Sykora, Jan, Kulig, Waldemar, Rog, Tomasz, Urem, Yagmur B., Abhinav, Abhinav, Danylchuk, Dmytro I., Hof, Martin, Klymchenko, Andrey S., Amaro, Mariana, Vattulainen, Ilpo, Sezgin, Erdinc

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Glucosylceramide modifies the LPS-induced inflammatory response in macrophages and the orientation of the LPS/TLR4 complex in silico by Mobarak, Edouard, Håversen, Liliana, Manna, Moutusi, Rutberg, Mikael, Levin, Malin, Perkins, Rosie, Rog, Tomasz, Vattulainen, Ilpo, Borén, Jan

“…Toll-like receptor 4 (TLR4) is activated by bacterial lipopolysaccharide (LPS), which drives the production of proinflammatory cytokines. Earlier studies have…”
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Dynamics and scaling of two-dimensional polymers in a dilute solution by Falck, E, Punkkinen, O, Vattulainen, I, Ala-Nissila, T

“…The breakdown of dynamical scaling for a dilute polymer solution in two dimensions has been suggested by Shannon and Choy [Phys. Rev. Lett. 79, 1455 (1997)]…”
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