Tapio Ala-Nissila

Collective and single particle diffusion on surfaces

We review in this article the current theoretical understanding of collective and single particle diffusion on surfaces and how it relates to the existing experimental data. We begin with a brief survey of the experimental techniques that have been employed for the measurement of the surface diffusion coefficients. This is followed by a section on the basic concepts involved in this field. In particular, we wish to clarify the relation between jump or exchange motion on microscopic length scales, and the diffusion coefficients which can be defined properly only in the long length and time scales. The central role in this is played by the memory effects. We also discuss the concept of diffusion under nonequilibrium conditions. In the third section, a variety of different theoretical approaches that have been employed in studying surface diffusion such as first principles calculations, transition state theory, the Langevin equation, Monte Carlo and molecular dynamics simulations, and path integral formalism are presented. These first three sections form an introduction to the field of surface diffusion. Section 4 contains subsections that discuss surface diffusion for various systems which have been investigated both experimentally and theoretically. The focus here is not so much on specific systems but rather on important issues concerning diffusion measurements or calculations. Examples include the influence of steps, diffusion in systems undergoing phase transitions, and the role of correlation and memory effects. Obviously, the choice of topics here reflects the interest and expertise of the authors and is by no means exhaustive. Nevertheless, these topics form a collection of issues that are under active investigation, with many important open questions remaining.

Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets in the parameterization. We refine the MARTINI procedure by including one additional target property related to the structure of the polymer, namely the radius of gyration. The force-field optimization is mainly based on experimental data. We test our procedure on polystyrene, a standard benchmark for coarse-grained (CG) polymer force-fields. Our model preserves the backbone-ring structure of the molecule, with each monomer represented by four CG beads. Structural properties in the melt are well reproduced, and their scaling with chain length agrees with the available experimental data. The time conversion factor between the CG and the atomistic simulations is nearly constant over a wide temperature range, and the CG force-field shows reasonable transferability between 350 and 600 K. The model is computationally efficient and polymer melts can be simulated over length scales of tens of nanometres and time scales of tens of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced.

Influence of polymer-pore interactions on translocation.

We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve the translocation probability. At the same time, it also increases the translocation time slowly for a weak attraction while an exponential dependence is observed for a strong attraction. For fixed driving force and chain length the histogram of translocation time has a transition from Gaussian distribution to long-tailed distribution with increasing attraction. Under a weak driving force and a strong attractive force, both the translocation time and the residence time in the pore show a nonmonotonic behavior as a function of the chain length. Our simulations results are in good agreement with recent experimental data.

Langevin dynamics simulations of polymer translocation through nanopores

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of an external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau(e) required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that tau(e) scales with the chain length N as tau(e) approximately N(1+2nu), where nu is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient xi, the driving force E, and the length of the chain N on the translocation time tau, which is defined as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and tau approximately E(-1). The influence of xi depends on the ratio between the driving and frictional forces. For intermediate xi, we find a crossover scaling for tau with N from tau approximately N(2nu) for relatively short chains to tau approximately N(1+nu) for longer chains. However, for higher xi, only tau approximately N(1+nu) is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing xi increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveal additional features of dependency on friction.

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.

The hydrophobic effect and its role in cold denaturation

The hydrophobic effect is considered the main driving force for protein folding and plays an important role in the stability of those biomolecules. Cold denaturation, where the native state of the protein loses its stability upon cooling, is also attributed to this effect. It is therefore not surprising that a lot of effort has been spent in understanding this phenomenon. Despite these efforts, many unresolved fundamental aspects remain. In this paper we review and summarize the thermodynamics of proteins, the hydrophobic effect and cold denaturation. We start by accounting for these phenomena macroscopically then move to their atomic-level description. We hope this review will help the reader gain insights into the role played by the hydrophobic effect in cold denaturation.

Microscopic mechanism for cold denaturation

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.

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 68meV 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.

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 [ital n] successive numbers. We apply the tests to show that recent errors in high precision Ising simulations using generalized feedback shift register algorithms are due to short range correlations in random number sequences.

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 numerically verify that asymptotically tau approximately N(1+2nu). 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.