Aaltodoc Repository :: Browsing by Author "Vattulainen, Ilpo"

Browsing by Author "Vattulainen, Ilpo"

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Atom-Scale Simulations of Alcohol-Membrane Interactions
(2006) Terämä, Emma M.; Vattulainen, Ilpo; Teknillisen fysiikan ja matematiikan osasto; Teknillinen korkeakoulu; Helsinki University of Technology; Nieminen, Risto
Cholesterol induces specific spatial and orientational order in cholesterol/phospholipid membranes
(2010) Martinez-Seara, Hector; Rog, Tomasz; Karttunen, Mikko; Reigada, Ramon; Vattulainen, Ilpo; Department of Applied Physics; Quantum Many-Body Physics
Background In lipid bilayers, cholesterol facilitates the formation of the liquid-ordered phase and enables the formation of laterally ordered structures such as lipid rafts. While these domains have an important role in a variety of cellular processes, the precise atomic-level mechanisms responsible for cholesterol's specific ordering and packing capability have remained unresolved. Methodology/Principal Findings Our atomic-scale molecular dynamics simulations reveal that this ordering and the associated packing effects in membranes largely result from cholesterol's molecular structure, which differentiates cholesterol from other sterols. We find that cholesterol molecules prefer to be located in the second coordination shell, avoiding direct cholesterol-cholesterol contacts, and form a three-fold symmetric arrangement with proximal cholesterol molecules. At larger distances, the lateral three-fold organization is broken by thermal fluctuations. For other sterols having less structural asymmetry, the three-fold arrangement is considerably lost. Conclusions/Significance We conclude that cholesterol molecules act collectively in lipid membranes. This is the main reason why the liquid-ordered phase only emerges for Chol concentrations well above 10 mol% where the collective self-organization of Chol molecules emerges spontaneously. The collective ordering process requires specific molecular-scale features that explain why different sterols have very different membrane ordering properties: the three-fold symmetry in the Chol-Chol organization arises from the cholesterol off-plane methyl groups allowing the identification of raft-promoting sterols from those that do not promote rafts.
Coarse-Grained Model for Phospholipid/Cholestrol Bilayer
(2004) Murtola, Teemu; Vattulainen, Ilpo; Falck, Emma; Teknillisen fysiikan ja matematiikan osasto; Teknillinen korkeakoulu; Helsinki University of Technology; Ala-Nissilä, Tapio
Biological membranes are complex systems with a large number of degrees of freedom. One of the main structural components of these membranes is a lipid bilayer. Computer simulations of lipid bilayers are very challenging: many interesting phenomena occur at much longer length and time scales than those accessible with atomic-level simulations. For studies beyond the microscopic regime, simplified coarse-grained models are therefore needed. We have constructed a simple, two-dimensional coarse-grained model for a lipid bilayer consisting of dipalmitoylphosphatidylcholine (DPPC) and cholesterol. The model has been constructed using a so-called Inverse Monte Carlo method, using results from atomic-level molecular dynamics simulations as input. The main goals have been to apply the Inverse Monte Carlo technique to lipid bilayers and find how it is suited for studying the large-scale properties of bilayers. In addition, we have explored the limitations of this approach. In our model each molecule is described by a single point-like particle. To find effective interactions for the coarse-grained particles, we have first performed detailed molecular dynamics simulations of the system at various cholesterol concentrations over a wide concentration range. We have then used the Inverse Monte Carlo method to construct effective interaction potentials for the particles. These potentials are constructed such that the radial distribution functions calculated from the coarse-grained system are identical to those calculated from the molecular dynamics simulations. Therefore the model gives correct results for structural properties at short length scales. Using the coarse-grained model, we have performed Monte Carlo simulations to study the large-scale structural properties of lipid bilayers. These results seem promising. We see evidence of formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations. This is in agreement with the phase diagram of the system. \\lork is still in progress to further understand the nature of this organisation. We have also found that the model is unable to describe the liquid crystalline to gel transition of pure DPPC bilayers. Additionally, we have learnt that the effective potentials are rather specific to both the concentration and temperature in which they were determined. We have also performed Brownian dynamics simulations to study general relationships between different diffusion coefficients. From these studies we can conclude that our approach for constructing coarse-grained models can be a useful tool in the future. It allows relatively easy adjustment of the level of coarse-graining, and it can be applied to various systems without major modifications. Also, our model could be improved in several ways to account for e.g. the ordering of the hydrocarbon tails of the DPPC molecules. Thus active research on the subject continues.
Comment on "Non-Arrhenius behavior of surface diffusion near a phase transition boundary" - Reply
(1998-06-15) Vattulainen, Ilpo; Merikoski, J.; Ala-Nissilä, Tapio; Ying, S.C.; Department of Applied Physics
A Reply to the Comment by C. Uebing and V. P. Zhdanov. Received 5 March 1998
Comment on Surface diffusion near the points corresponding to continuous phase transitions
(AIP Publishing, 1999) Vattulainen, Ilpo; Ying, S. C.; Ala-Nissilä, Tapio; Merikoski, J.; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
It is well known that unlike static equilibrium properties, kinetic quantities in Monte Carlo simulations are very sensitive to the details of the algorithm used for the microscopic transition rates. This is particularly true near the critical region where fluctuations are pronounced. We demonstrate that when diffusion of oxygen adatoms near the order–disorder transition of a lattice-gas model of the O/W(110) model system is studied, the transition rates must be chosen carefully. In particular, we show that the choice by Uebing and Zhdanov [J. Chem. Phys. 109, 3197 (1998)] is inappropriate for the study of critical effects in diffusion.
Density Profile Evolution and Nonequilibrium Effects in Partial and Full Spreading Measurements of Surface Diffusion
(AIP Publishing, 2001) Nikunen, P.; Vattulainen, Ilpo; Ala-Nissilä, Tapio; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
We study the nature of nonequilibrium effects in the collective diffusion coefficient DC(θ) vs the coverage θ as extracted from Boltzmann–Matano analysis of spreading coverage profiles. We focus on the temporal behavior of the profiles and study how the corresponding nonequilibrium effects in DC(θ) depend on the initial density gradient and the initial state from which the spreading starts. To this end, we carry out extensive Monte Carlo simulations for a lattice-gas model of the O/W(110) system. Studies of submonolayer spreading from an initially ordered p(2×1) phase at θ=12 reveal that the spreading and diffusion rates in directions parallel and perpendicular to rows of oxygen atoms are significantly different within the ordered phase. Aside from this effect, we find that the degree of ordering in the initial phase has a relatively small impact on the overall behavior of DC(θ). Also, although we find that nonequilibrium effects are clearly present in submonolayer spreading profiles, DC(θ) determined from such data approaches its asymptotic equilibrium behavior much more rapidly than in the case of full spreading. Nevertheless, in both cases there are noticeable deviations from equilibrium results that persist even at very long times and are strongest in ordered phases and in the vicinity of phase boundaries. These conclusions are confirmed by complementary studies of the temporal behavior of the order parameter φ(θ). Finally, we use DC(θ) and φ(θ) to determine the locations of phase boundaries and find such data to be clearly time dependent during full spreading. We conclude that nonequilibrium effects seem to be an inherent feature in profile evolution studies of surface diffusion in all cases where ordering plays a prominent role. This warrants particular care to be taken with profile spreading experiments.
Dynamics and Scaling of Polymers in a Dilute Solution: Analytical Treatment in Two and Higher Dimensions
(AIP Publishing, 2005) Punkkinen, O.; Falck, E.; Vattulainen, Ilpo; Ala-Nissilä, Tapio; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
We consider the dynamical scaling of a single polymer chain in good solvent. In the case of two-dimensional systems, Shannon and Choy [Phys. Rev. Lett.79, 1455 (1997)] have suggested that the dynamical scaling for a dilute polymer solution breaks down. Using scaling arguments and analytical calculations based on the Zimm model, we show that the dynamical scaling of a dilute two-dimensional polymer system holds when the relevant dynamical quantities are properly extracted from finite systems. Most important, the polymerdiffusion coefficient in two dimensions scales logarithmically with system size, in excellent agreement with our extensive computer simulations. This scaling is the reason for the failure of the previous attempts to resolve the dynamical scaling of dilute two-dimensional polymer systems. In three and higher dimensions our analytic calculations are in agreement with previous results in the literature.
Dynamics and scaling of two-dimensional polymers in a dilute solution
(American Physical Society (APS), 2003) Falck, E.; Punkkinen, O.; Vattulainen, Ilpo; Ala-Nissilä, Tapio; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
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)]. However, we show here through extensive computer simulations that dynamical scaling holds when the relevant dynamical quantities are properly extracted from finite systems. To verify dynamical scaling, we present results based on mesoscopic simulations in two dimensions for a polymer chain in a good solvent with full hydrodynamic interactions. We also present analytical arguments for the size dependence of the diffusion coefficient and find excellent agreement with the present large-scale simulations.
Effects of quenched impurities on surface diffusion, spreading and ordering of O/W(110)
(AIP Publishing, 2002) Nikunen, P.; Vattulainen, Ilpo; Ala-Nissilä, Tapio; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
We study how quenched impurities affect the surfacediffusion and ordering of strongly interactingadsorbate atoms on surfaces. To this end, we carry out Monte Carlo simulations for a lattice-gas model of O/W(110), including small concentrations of immobile impurities which block their adsorption sites. We examine the behavior of the diffusion coefficients and order parameters as a function of coverage corresponding to various ordered phases at low temperatures. The effects of impurities are examined under both equilibrium and nonequilibrium conditions, and the results are compared to recent studies on a completely clean surface. We find that even minute impurity concentrations affect the diffusion behavior considerably in equilibrium. The effects are strongest in ordered phases and close to phase boundaries, where quenched impurities lead to a reduction of order, which in turn leads to significant changes in the collective diffusion and phase behavior. As the impurity concentration is increased to a level of a few percent of the total surface area, the reduction in order becomes particularly prominent at high coverages. Further studies under nonequilibrium conditions reveal that nonequilibrium effects are strong in the absence of impurities, while for surfaces covered by impurities the nonequilibrium effects are relatively weaker.
From molten globule to swollen coil: Simulations of a lone polymer chain in an explicit solvent
(2004) Miettinen, Markus; Karttunen, Mikko; Vattulainen, Ilpo; Sähkö- ja tietoliikennetekniikan osasto; Teknillinen korkeakoulu; Helsinki University of Technology; Kaski, Kimmo
Polymeerit ovat suuria ketjumaisia molekyylejä, joissa useat pienemmät molekyylit eli monomeerit ovat liittyneet toisiinsa kemiallisin sidoksin. Polymeeriketjun pituus on selvästi yksittäisen monomeerin kokoa suurempi. Polymeeriliuosten fysikaaliset ominaisuudet määräytyvät pitkälti ketjujen konformaatioiden perusteella, ja siksi niillä on monia kiehtovia ominaisuuksia, joita ei havaita yksinkertaisilla nesteillä. Eräs näistä on ketjujen muodonmuutos pisaramaisesta konformaatiosta löyhäksi vyyhdeksi, kun liuottimen laatu muuttuu huonosta hyväksi. Tällä transitiolla on selvä vaikutus myös polymeeriliuoksen makroskooppisiin ominaisuuksiin. Tässä diplomityössä läpikäyn joitakin teoreettisen polymeerifysiikan perusteita. Lisäksi käsittelen molekyylidynamiikaksi kutsutun simulaatiomenetelmän teoriaa ja erityisesti niitä haasteita, joita kohdataan pyrittäessä simuloimaan epätasapainossa olevia tai epä-Hamiltonisia systeemejä. Molempien kokonaisuuksien esittelyssä pyrin yksityiskohtaiseen analyyttiseen tarkasteluun. Työn laskennallisessa osuudessa paneudun liuottimen laadun vaikutuksiin eli tutkin ketjun ominaisuuksia eri lämpötiloissa ja vuorovaikutuspotentiaaleissa. Käsittelen laajan kirjon polymeerikonformaatioita, alkaen pisaramaisista ja edeten ideaalisten ketjujen kautta vyyhtimäisiin. Välttääkseni ongelmat, joita aiheutuu polymeerien saostumisesta kiinni toisiinsa huonoissa liuottimissa, keskityn äärettömän laimeisiin liuoksiin eli tarkastelen vain yhtä vapaata ketjua eksplisiittisesti kuvatussa monomeerisessa liuottimessa. Tehdyt simulaatiot paljastavat, että valitussa mallissa liuottimen transitio kaasusta nesteeksi ja polymeerin transitio löyhäksi vyyhdeksi tapahtuvat samalla lämpötila-alueella. Tulokset osoittavat kuitenkin, että valitsemalla simulaatiolämpötila sopivasti polymeerin koko transitiota pisarasta vyyhdeksi voidaan tarkastella säätämällä vuorovaikutuspotentiaalin voimakkuutta.
High Density Lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy
(2011) Yetukuri, Laxman; Huopaniemi, Ilkka; Koivuniemi, Artturi; Maranghi, Marianna; Hiukka, Anne; Nygren, Heli; Kaski, Samuel; Taskinen, Marja-Riitta; Vattulainen, Ilpo; Jauhiainen, Matti; Oresic, Matej; Helsinki Insititute for Information Technology HIIT; Tietojenkäsittelytieteen laito; Department of Applied Physics
In a recent FIELD study the fenofibrate therapy surprisingly failed to achieve significant benefit over placebo in the primary endpoint of coronary heart disease events. Increased levels of atherogenic homocysteine were observed in some patients assigned to fenofibrate therapy but the molecular mechanisms behind this are poorly understood. Herein we investigated HDL lipidomic profiles associated with fenofibrate treatment and the drug-induced Hcy levels in the FIELD substudy. We found that fenofibrate leads to complex HDL compositional changes including increased apoA-II, diminishment of lysophosphatidylcholines and increase of sphingomyelins. Ethanolamine plasmalogens were diminished only in a subgroup of fenofibrate-treated patients with elevated homocysteine levels. Finally we performed molecular dynamics simulations to qualitatively reconstitute HDL particles in silico. We found that increased number of apoA-II excludes neutral lipids from HDL surface and apoA-II is more deeply buried in the lipid matrix than apoA-I. In conclusion, a detailed molecular characterization of HDL may provide surrogates for predictors of drug response and thus help identify the patients who might benefit from fenofibrate treatment.
Interplay between steps and nonequilibrium effects in surface diffusion for a lattice-gas model of O/W(110)
(AIP Publishing, 2007) Masin, M.; Vattulainen, Ilpo; Ala-Nissilä, Tapio; Chvoj, Z.; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
The authors consider the influence of steps and nonequilibrium conditions on surfacediffusion in a strongly interactingsurfaceadsorbate system. This problem is addressed through Monte Carlo simulations of a lattice-gas model of O∕W(110), where steps are described by an additional binding energy EB at the lower step edge positions. Both equilibrium fluctuation and Boltzmann-Matano spreading studies indicate that the role of steps for diffusion across the steps is prominent in the ordered phases at intermediate coverages. The strongest effects are found in the p(2×1) phase, whose periodicity Lp is 2. The collective diffusion then depends on two competing factors: domain growth within the ordered phase, which on a flat surface has two degenerate orientations [p(2×1) and p(1×2)], and the step-induced ordering due to the enhanced binding at the lower step edge position. The latter case favors the p(2×1) phase, in which all adsorption sites right below the step edge are occupied. When these two factors compete, two possible scenarios emerge. First, when the terrace width L does not match the periodicity of the ordered adatom layer (L/Lp is noninteger), the mismatch gives rise to frustration, which eliminates the effect of steps provided that EB is not exceptionally large. Under these circumstances, the collective diffusion coefficient behaves largely as on a flat surface. Second, however, if the terrace width does match the periodicity of the ordered adatom layer (L/Lp is an integer), collective diffusion is strongly affected by steps. In this case, the influence of steps is manifested as the disappearance of the major peak associated with the ordered p(2×1) and p(1×2) structures on a flat surface. This effect is particularly strong for narrow terraces, yet it persists up to about L≈25Lp for small EB and up to about L≈500Lp for EB, which is of the same magnitude as the bare potential of the surface. On real surfaces, similar competition is expected, although the effects are likely to be smaller due to fluctuations in terrace widths. Finally, Boltzmann-Matano spreading simulations indicate that even slight deviations from equilibrium conditions may give rise to transient peaks in the collective diffusion coefficient. These transient structures are due to the interplay between steps and nonequilibrium conditions and emerge at coverages, which do not correspond to the ideal ordered phases.
Lateral pressure profile calculations of lipid membranes from atomic scale molecular dynamics simulations
(2006) Ollila, Samuli; Hyvönen, Marja; Vattulainen, Ilpo; Teknillisen fysiikan ja matematiikan osasto; Teknillinen korkeakoulu; Helsinki University of Technology; Ala-Nissilä, Tapio
Muutaman nanometrin paksuiset solukalvot sisältävät useita erilaisia molekyylejä (esim. rasvoja, proteiineja ja sokereita). Solukalvon perusrakenteen muodostaa lipidimolekyyleistä muodostuva kaksoiskalvo, mutta funktionaaliset ominaisuudet ovat pääasiassa proteiinien säätelemiä. Proteiinien funktionaalisuuden on kuitenkin huomattu riippuvan ympäristön lipidimolekyyleistä, joten myös puhtaan solukalvokerroksen ominaisuudet saattavat olla funktionaalisesti merkittäviä. Vielä ei kuitenkaan tiedetä miksi ja miten ympärillä olevat lipidit vaikuttavat proteiinien toimintaan. 1990-luvun lopussa esitetyn hypoteesin mukaan painejakauman muutokset lipidikaksoiskerroksessa saattavat aiheuttaa muutoksia proteiinien toiminnassa. Tämän hypoteesin testaus on kuitenkin hankalaa, koska paine-eroja pienien etäisyyksien (~10^{-9 m) välillä ei pystytä vielä kokeellisesti mittaamaan ja paikallisen paineen määritteleminen teoreettisesti näillä etäisyyksillä on hankalaa.

Painejakauma kaksoiskerroksen sisällä on kiinnostava myös yleisemmällä tasolla, koska se yhdistää mikroskooppiset kaksoiskerroksen ominaisuudet kalvon jatkumo-ominaisuuksiin.

Tässä työssä on kehitetty menetelmä painejakauman laskemiseksi lipidikaksoiskerroksen sisällä käyttäen atomitason molekyylidynamiikkamenetelmää.
Myös kaksoissidosten vaikutusta painejakaumaan tutkittiin ja havaittiin, että kaksoissidokset pienentävät painetta kaksoiskerroksen sisällä, mikä saattaa selittää havaitun kaksoissidosten vaikutuksen kalvoproteiinien toimintaan.}
Memory effects and coverage dependence of surface diffusion in a model adsorption system
(American Physical Society (APS), 1999) Vattulainen, Ilpo; Ying, S. C.; Ala-Nissilä, Tapio; Merikoski, J.; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
We study the coverage dependence of surface diffusion coefficients for a strongly interacting adsorption system O/W(110) via Monte Carlo simulations of a lattice-gas model. In particular, we consider the nature and emergence of memory effects as contained in the corresponding correlation factors in tracer and collective diffusion. We show that memory effects can be very pronounced deep inside the ordered phases and in regions close to first and second order phase transition boundaries. Particular attention is paid to the details of the time dependence of memory effects. The memory effect in tracer diffusion is found to decay following a power law after an initial transient period. This behavior persists until the hydrodynamic regime is reached, after which the memory effect decays exponentially. The time required to reach the hydrodynamical regime and the related exponential decay is strongly influenced by both the critical effects related to long-wavelength fluctuations and the local order in the overlayer. We also analyze the influence of the memory effects on the effective diffusion barriers extracted from the Arrhenius analysis. For tracer diffusion, we find that the contribution from memory effects can be as large as 50% to the total barrier. For collective diffusion, the role of memory effects is in general less pronounced.
Memory expansion for diffusion coefficients
(American Physical Society (APS), 1998) Ying, S. C.; Vattulainen, Ilpo; Merikoski, J.; Hjelt, T.; Ala-Nissilä, Tapio; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
We present a memory expansion for macroscopic transport coefficients such as the collective and tracer diffusion coefficients DC and DT, respectively. The successive terms in this expansion for DC describe rapidly decaying memory effects of the center-of-mass motion, leading to fast convergence when evaluated numerically. For DT, one obtains an expansion of similar form that contains terms describing memory effects in single-particle motion. As an example we evaluate DC and DT for three strongly interacting surface systems through Monte Carlo simulations, and for a simple model diffusion system via molecular dynamics calculations. We show that the numerical method provides a speedup of about two orders of magnitude in computational time as compared with the standard methods, when collective diffusion is concerned. For tracer diffusion, the speedup is not quite as significant. Our studies using the memory expansion provide information of the nature of memory effects in diffusion and suggest a nontrivial power-law behavior of memory terms at intermediate times. We also discuss the application of the present approach to studies of other transport coefficients.
Microscopic Mechanism for Cold Denaturation
(American Physical Society (APS), 2008) Dias, Cristiano L.; Ala-Nissilä, Tapio; Karttunen, Mikko; Vattulainen, Ilpo; Grant, Martin; Teknillisen fysiikan laitos; Department of Applied Physics; Perustieteiden korkeakoulu; School of Science
We elucidate the mechanism of cold denaturation through constant-pressure simulations for a model of hydrophobic molecules in an explicit solvent. We find that the temperature dependence of the hydrophobic effect induces, facilitates, and is the driving force for cold denaturation. The physical mechanism underlying this phenomenon is identified as the destabilization of hydrophobic contact in favor of solvent-separated configurations, the same mechanism seen in pressure-induced denaturation. A phenomenological explanation proposed for the mechanism is suggested as being responsible for cold denaturation in real proteins.
Non-exponential dacay of velocity correlations in surface diffusion: The role of interactions and ordering
(2000) Vattulainen, Ilpo; Hjelt, T.; Ala-Nissilä, T.; Ying, S.C; Department of Applied Physics
We study the diffusive dynamics of adparticles in two model systems with strong interactions by considering the decay of the single-particle velocity correlation function φ(t). In accordance with previous studies, we find φ(t) to decay nonexponentially and follow a power-law φ(t)∼t−x at intermediate times t, while at long times there is a crossover to an exponential decay. We characterize the behavior of the decay exponent x in detail in various ordered phases and in the vicinity of phase boundaries. We find that within the disordered phase, the behavior of x can be rationalized in terms of interaction effects. Namely, x is typically larger than two in cases where repulsive adparticle–adparticle interactions dominate, while attractive interactions lead to x<2. In ordered phases, our results suggest that the behavior of x is mainly governed by ordering effects that determine the local structure in which adatoms diffuse. Then the decay is characterized by 1
Nonequilibrium effects in diffusion of interacting particles on vicinal surfaces
(AIP Publishing, 2005) Masin, M.; Vattulainen, Ilpo; Ala-Nissilä, Tapio; Chvoj, Z.; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
We study the influence of nonequilibrium conditions on the collective diffusion of interacting particles on vicinal surfaces. To this end, we perform Monte Carlo simulations of a lattice-gas model of an ideal stepped surface, where adatoms have nearest-neighbor attractive or repulsive interactions. Applying the Boltzmann–Matano method to spreading density profiles of the adatoms allows the definition of an effective, time-dependent collective diffusion coefficient DtC(θ) for all coverages θ. In the case of diffusion across the steps and strong binding at lower step edges we observe three stages in the behavior of the corresponding Dtxx,C(θ). At early times when the adatoms have not yet crossed the steps, Dtxx,C(θ) is influenced by the presence of steps only weakly. At intermediate times, where the adatoms have crossed several steps, there are sharp peaks at coverages θ<1∕L and θ>1−1∕L, where L is the terrace width. These peaks are due to different rates of relaxation of the density at successive terraces. At late stages of spreading, these peaks vanish and Dtxx,C(θ) crosses over to its equilibrium value, where for strong step edge binding there is a maximum at θ=1∕L. In the case of diffusion in direction along the steps the nonequilibrium effects in Dtyy,C(θ) are much weaker, and are apparent only when diffusion along ledges is strongly suppressed or enhanced.
Nonexponential decay of velocity correlations in surface diffusion: The role of interactions and ordering
(AIP Publishing, 2000) Vattulainen, Ilpo; Hjelt, T.; Ala-Nissilä, Tapio; Ying, S. C.; Department of Applied Physics; Teknillisen fysiikan laitos; Perustieteiden korkeakoulu; School of Science
We study the diffusive dynamics of adparticles in two model systems with strong interactions by considering the decay of the single-particle velocity correlation functionφ(t). In accordance with previous studies, we find φ(t) to decay nonexponentially and follow a power-law φ(t)∼t−x at intermediate times t, while at long times there is a crossover to an exponential decay. We characterize the behavior of the decay exponent x in detail in various ordered phases and in the vicinity of phase boundaries. We find that within the disordered phase, the behavior of x can be rationalized in terms of interaction effects. Namely, x is typically larger than two in cases where repulsive adparticle–adparticle interactions dominate, while attractive interactions lead to x<2. In ordered phases, our results suggest that the behavior of x is mainly governed by ordering effects that determine the local structure in which adatoms diffuse. Then the decay is characterized by 1
Structural Analysis of Lipid Molecules in Cell Membranes by Self-Organizing Maps
(2006) Kupiainen, Mikko; Vattulainen, Ilpo; Falck, Emma; Teknillisen fysiikan ja matematiikan osasto; Teknillinen korkeakoulu; Helsinki University of Technology; Ala-Nissilä, Tapio
Solukalvot ympäröivät kaikkia eläviä soluja ja soluelimiä, ja ne ovat siten äärimmäisen tärkeitä rakenteita kaikille elollisille organismeille. Biomembraanit eivät ole passiivisia rakenteita, vaan niillä on tärkeä rooli muun muassa säätelemässä molekyylien kulkua solun ja sen ympäristön välillä. Biomembraanin tärkein rakenneosa on lipidikaksoiskerros, joka muodostuu miljardeista yksittäisistä lipidimolekyyleistä. Lipidimolekyyleillä on useita vapausasteita, ja niitä voi siten kuvata suuri määrä erilaisia konformaatioita. Lipidimolekyylien konformaatiotilojen oletetaan liittyvän moniin tärkeisiin biomembraanien rakenteellisiin, dynaamisiin ja funktionaalisiin ominaisuuksiin. Pienestä mittakaavasta johtuen konformaatioiden yksityiskohtaisia ominaisuuksia ei voida tutkia kokeellisesti. Tietokonesimulaatiot kuitenkin tarjoavat atomitason tietoa konformaatiotilojen käyttäytymisestä. Tässä työssä on tutkittu itsejärjestyvien karttojen käyttämistä lipidikonformaatioiden analysoimisessa. Lähtötietona on käytetty molekyylidynamiikkasimulaatiosta saatavaa atomitason dataa. Työssä on keskitytty menetelmän kehittämiseen, tutkittu koulutusparametrien vaikutusta tulosten laatuun, sekä selvitetty kartan koon vaikutusta lopputulokseen. Menetelmää on sovellettu 50 nanosekunnin pituisen PLPC-lipidikaksoiskerrossimulaation konformaatioiden tutkimiseen. Työssä PLPC:n pääryhmän, glyseroliosan ja tyydyttymättömän hiilivetyhännän konformaatioita on tutkittu erikseen. Tärkeimmät konformaatiotilat sekä tietyt pienemmät yksityiskohdat löytyivät vaivatta jokaisessa tapauksessa. Työssä on myös tutkittu konformaatioiden dynamiikkaa ja verrattu tuloksia aiempaan tutkimukseen. Tulokset osoittavat, että itsejärjestyvät kartat ovat suhteellisen yksinkertainen ja luotettava menetelmä, jolla voidaan nopeasti selvittää systeemin tärkeimmät ominaispiirteet kvalitatiivisella tasolla. Menetelmän käyttö ei vaadi lainkaan ennakkotuntemusta systeemin käyttäytymisestä. Tulevalle tutkimukselle on monia suuntia. Menetelmän käyttämän algoritmin toteuttamista voidaan kehittää, mikä mahdollistaisi laajempien systeemien analysoimisen. Mielenkiintoinen kohde jatkotutkimukselle on tarkastella tässä työssä esitellyillä menetelmillä muita lipidisysteemejä, esimerkiksi monityydyttymättömän lipidihännän käyttäytymistä. Itsejärjestyviä karttoja voisi myös käyttää eri lipidityyppien välisten vuorovaikutusmekanismien tutkimiseen. Kohteena voisi olla esimerkiksi fosfolipidin ja kolesterolin vuorovaikutus. Mielenkiintoista olisi myös käyttää analyysistä saatuja systeemin tärkeimpiä konformaatiotiloja esittämään konformaatiovapausasteita karkeistetussa simulaatiomallissa.

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