Biomedical subjects

T Ala-Nissila

Publications and source records attributed to T Ala-Nissila.

At least 19 recordsLinked to original sources

PubMed2006

Interface equations for capillary rise in random environment.

We consider the influence of quenched noise upon interface dynamics in two-dimensional (2D) and 3D capillary rise with rough walls by using a phase-field approach, where the local conservation of mass in the bulk is explicitly included. In the 2D case, the disorder is assumed to be in the effective mobility coefficient, while in the 3D case we explicitly consider the influence of locally fluctuating geometry along a solid wall using a generalized curvilinear coordinate transformation. To obtain the equations of motion for meniscus and contact lines, we develop a systematic projection formalism that allows inclusion of disorder. Using this formalism, we derive linearized equations of motion for the meniscus and contact line variables, which become local in the Fourier space representation. These dispersion relations contain effective noise that is linearly proportional to the velocity. The deterministic parts of our dispersion relations agree with results obtained from other similar studies in the proper limits. However, the forms of the noise terms derived here are quantitatively different from the other studies.

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PubMed2006

Phase diagram and commensurate-incommensurate transitions in the phase field crystal model with an external pinning potential.

We study the phase diagram and the commensurate-incommensurate transitions in a phase field model of a two-dimensional crystal lattice in the presence of an external pinning potential. The model allows for both elastic and plastic deformations and provides a continuum description of lattice systems, such as for adsorbed atomic layers or two-dimensional vortex lattices. Analytically, a mode expansion analysis is used to determine the ground states and the commensurate-incommensurate transitions in the model as a function of the strength of the pinning potential and the lattice mismatch parameter. Numerical minimization of the corresponding free energy shows reasonable agreement with the analytical predictions and provides details on the topological defects in the transition region. We find that for small mismatch the transition is of first order, and it remains so for the largest values of mismatch studied here. Our results are consistent with results of simulations for atomistic models of adsorbed overlayers.

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PubMed2006

Polymer translocation through a nanopore: a two-dimensional Monte Carlo study.

We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau required for the polymer to completely exit the pore on either end. We find numerically that tau scales with the chain length N as tau approximately N(1+2nu), where nu is the Flory exponent. This is the same scaling as predicted for the translocation time of a polymer which passes through the nanopore in one direction only. We examine the interplay between the pore length L and the radius of gyration R(g). For L< >R(g), we find tau approximately N. In addition, we numerically find the scaling function describing crossover between short and long pores. We also show that tau has a minimum as a function of L for longer chains when the radius of gyration along the pore direction R( parallel) approximately L. Finally, we demonstrate that the stiffness of the polymer does not change the scaling behavior of translocation dynamics for single-segment dynamics.

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PubMed2005

Nonequilibrium effects in diffusion of interacting particles on vicinal surfaces.

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 D(C) (t)(theta) for all coverages theta. 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 D(xx,C) (t)(theta). At early times when the adatoms have not yet crossed the steps, D(xx,C) (t)(theta) 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 theta<1L and theta>1-1L, 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 D(xx,C) (t)(theta) crosses over to its equilibrium value, where for strong step edge binding there is a maximum at theta=1L. In the case of diffusion in direction along the steps the nonequilibrium effects in D(yy,C) (t)(theta) are much weaker, and are apparent only when diffusion along ledges is strongly suppressed or enhanced.

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PubMed2005

Strain relief in Cu-Pd heteroepitaxy.

We present experimental and theoretical studies of Pd/Cu(100) and Cu/Pd(100) heterostructures in order to explore their structure and misfit strain relaxation. Ultrathin Pd and Cu films are grown by pulsed laser deposition at room temperature. For Pd/Cu, compressive strain is released by networks of misfit dislocations running in the [100] and [010] directions, which appear after a few monolayers (ML) already. In striking contrast, for Cu/Pd the tensile overlayer remains coherent up to about 9 ML, after which multilayer growth occurs. The strong asymmetry between tensile and compressive cases is in contradiction with continuum elasticity theory and is also evident in the structural parameters of the strained films. Molecular dynamics calculations based on classical many-body potentials confirm the pronounced tensile-compressive asymmetry and are in good agreement with the experimental data.

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PubMed2005

Dynamics and scaling of polymers in a dilute solution: analytical treatment in two and higher dimensions.

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 polymer diffusion 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.

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PubMed2004

Sedimentation dynamics of spherical particles in confined geometries.

We study the steady-state dynamics of sedimenting non-Brownian particles in confined geometries with full hydrodynamic interactions at small but finite Reynolds numbers. We employ extensive computer simulations using a method where a continuum liquid phase is coupled through Stokesian friction to a discrete particle phase. In particular, we consider a sedimentation box which is otherwise periodic except that it is confined by two parallel walls parallel to gravity with a spacing Lx. By systematically varying Lx we explore the change in dynamics from a quasi-two-dimensional (2D) case to a three-dimensional case. We find that in such confined geometries there is a depletion of particle number density at the walls for small volume fractions, while for large volume fractions there is an excess number of particles at the walls. For the average sedimentation velocity, we find that the Richardson-Zaki law is well obeyed but the decrease of the velocity for dilute systems is slower for smaller values of Lx. We study the anisotropy of the velocity fluctuations and find that in the direction of gravity there is excellent agreement with the predicted scaling with respect to Lx. We also find that the behavior of the corresponding diffusion coefficients as a function of Lx is qualitatively different in the direction parallel to gravity and perpendicular to it. In the quasi-2D limit where particles block each other, the velocity fluctuations behave differently from the other confined systems.

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PubMed2004

Submonolayer growth with anomalously high island density in hyperthermal deposition.

We present a rate equation model for submonolayer island growth under conditions where hyperthermal deposition techniques such as low-energy ion deposition are employed to achieve smooth layer-by-layer growth. By asymptotic analysis, we demonstrate that the model exhibits stationary behavior with well-defined dynamic and growth exponents beta and chi, respectively, in the limit of small and high detachment rates. We verify these predictions by using the particle coalescence simulation method. The simulations reveal the existence of a relatively sharp transition regime with an increasing detachment rate of adatoms from high values of the growth exponent beta approximately 1 to much smaller values of beta determined by detachment and island diffusion processes. Our numerical results for the island size distribution indicate an anomalously high number of small islands, in agreement with available experimental data.

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PubMed2004

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 DT(rho)/D0 and DC(rho)/D0 respectively, where D0 is the single-particle diffusion coefficient, as a function of the density of the colloids rho. At low Schmidt numbers Sc - 1, we find that hydrodynamics has essentially no effect on the behaviour of DT (rho)/D0. At larger Sc, DT (rho)/D0 seems to be enhanced at all densities, although the differences compared to the case without hydrodynamics are rather 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 without hydrodynamic interactions.

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PubMed2003

Dynamics and scaling of two-dimensional polymers in a dilute solution.

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.

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PubMed2003

Collective effects in settling of spheroids under steady-state sedimentation.

We study the settling dynamics of non-Brownian prolate spheroids under steady-state sedimentation. We consider the case of moderate particle Reynolds numbers properly taking into account the hydrodynamic effects. For small volume fractions, we find an orientational transition of the spheroids, characterized by enhanced density fluctuations. Around the transition, the average settling velocity has a maximum which may even exceed the terminal velocity of a single spheroid, in accordance with experiments.

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PubMed2002

Exact and efficient discrete random walk method for time-dependent two-dimensional environments.

We present an exact method for speeding up random walk in two-dimensional complicated lattice environments. To this end, we derive the discrete two-dimensional probability distribution function for a diffusing particle starting at the center of a square of linear size s. This is used to propagate random walkers from the center of the square to sites which are nearest neighbors to its perimeter sites, thus saving O(s(2)) steps in numerical simulations. We discuss in detail how this method can be implemented efficiently. We examine its performance in the diffusion limited aggregation model which produces fractal structures, and in a one-sided step-growth model producing compact, fingerlike structures. We show that in both cases, the square propagator method reduces the computational effort by a factor proportional to the linear system size as compared to standard random walk.

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PubMed2002

Interface dynamics and kinetic roughening in fractals.

We consider the dynamics and kinetic roughening of single-valued interfaces in two-dimensional fractal media. Assuming that the local height difference distribution function of the fronts obeys Levý statistics with a well-defined power-law decay exponent, we derive analytic expressions for the local scaling exponents. We also show that the kinetic roughening of the interfaces displays anomalous scaling and multiscaling in the relevant correlation functions. For invasion percolation models, the exponents can be obtained from the fractal geometry of percolation clusters. Our predictions are in excellent agreement with numerical simulations.

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PubMed2002

Surface diffusion anomaly near a substrate phase transition: H on W(100).

Using a linear optical diffraction method, we have experimentally studied the long predicted diffusion anomalous behavior for H/W(100) near the reconstructive phase transition of the W(100) substrate. This anomaly manifests itself in the form of a strong dip in the diffusion coefficient D at the transition temperature T(C). We interpret the strong reduction of D as a result of the diverging friction damping near the transition. The finite dip in D instead of a vanishing D at T(C) also demonstrates the importance of the non-Markovian (memory) deviation from the simple instantaneous damping picture.

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PubMed2002

Finding transition paths and rate coefficients through accelerated Langevin dynamics.

We present a technique to resolve the rare event problem for a Langevin equation describing a system with thermally activated transitions. A transition event within a given time interval (0,t(f)) can be described by a transition path that has an activation part during (0,t(M)) and a deactivation part during (t(M),t(f))(0<t(M)<t(f)). The activation path is governed by a Langevin equation with negative friction while the deactivation path by the standard Langevin equation with positive friction. Each transition path carries a given statistical weight from which rate constants and related physical quantities can be obtained as averages over all possible paths. We demonstrate how this technique can be used to calculate activation rates of a particle in a two dimensional potential for a wide range of temperatures where standard molecular dynamics techniques are inefficient.

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PubMed2002

Energetics and vibrational states for hydrogen on Pt(111).

We present a combination of theoretical calculations and experiments for the low-lying vibrational excitations of H and D atoms adsorbed on the Pt(111) surface. The vibrational band states are calculated based on the full three-dimensional adiabatic potential energy surface obtained from first-principles calculations. For coverages less than three quarters of a monolayer, the observed experimental high-resolution electron peaks at 31 and 68 meV are in excellent agreement with the theoretical transitions between selected bands. Our results convincingly demonstrate the need to go beyond the local harmonic oscillator picture to understand the dynamics of this system.

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PubMed2001

Interface pinning in spontaneous imbibition.

Evaporation and gravity induced pinning in spontaneous imbibition are examined within a phase field formalism. Evaporation is introduced via a nonconserving term and gravity through a convective term that constrains the influx of liquid. Their effects are described by dimensionless coupling constants epsilon and g, respectively. From liquid conservation, the early time behavior of the average interface position follows H(t) approximately t1/2 until a crossover time t*(g,epsilon). After that the pinning height Hp(g,epsilon) is approached exponentially in time, in accordance with mean field theory. The statistical roughness of the interface is described by an exponent chi approximately 1.25 at all stages of the rise, but the dynamic length scale controlling roughness crosses over from xi(x) approximately H1/2 to a time independent pinning length scale xi(p)(epsilon,g).

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PubMed2001

Kinetic roughening in slow combustion of paper.

Results of experiments on the dynamics and kinetic roughening of one-dimensional slow-combustion fronts in three grades of paper are reported. Extensive averaging of the data allows a detailed analysis of the spatial and temporal development of the interface fluctuations. The asymptotic scaling properties, on long length and time scales, are well described by the Kardar-Parisi-Zhang (KPZ) equation with short-range, uncorrelated noise. To obtain a more detailed picture of the strong-coupling fixed point, characteristic of the KPZ universality class, universal amplitude ratios, and the universal coupling constant are computed from the data and found to be in good agreement with theory. Below the spatial and temporal scales at which a crossover takes place to the standard KPZ behavior, the fronts display higher apparent exponents and apparent multiscaling. In this regime the interface velocities are spatially and temporally correlated, and the distribution of the magnitudes of the effective noise has a power-law tail. The relation of the observed short-range behavior and the noise as determined from the local velocity fluctuations is discussed.

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