How to mesh up Ewald sums (II): An accurate error estimate for the P3M algorithm

We construct an accurate estimate for the root mean square force error of the particle-particle-particle-mesh (P3M) algorithm by extending a single particle pair error measure which has been given by Hockney and Eastwood. We also derive an easy-to-use analytic approximation to the error formula. This allows a straightforward and precise determination of the optimal splitting parameter (as a function of system specifications and P3M parameters) and hence knowledge of the force accuracy prior to the actual simulation. The high quality of the estimate is demonstrated in several examples.Comment: 9 pages, 7 figures included, revtex styl

Attraction and ionic correlations between charged stiff polyelectrolytes

We use Molecular Dynamics simulations to study attractive interactions and the underlying ionic correlations between parallel like-charged rods in the absence of additional salt. For a generic bulk system of rods we identify a reduction of short range repulsions as the origin of a negative osmotic coefficient. The counterions show signs of a weak three-dimensional order in the attractive regime only once the rod-imposed charge-inhomogeneities are divided out. We also treat the case of attraction between a single pair of rods for a few selected line charge densities and rod radii. Measurements of the individual contributions to the force between close rods are studied as a function of Bjerrum length. We find that even though the total force is always attractive at sufficiently high Bjerrum length, the electrostatic contribution can ultimately become repulsive. We also measure azimuthal and longitudinal correlation functions to answer the question how condensed ions are distributed with respect to each other and to the neighboring rod. For instance, we show that the prevalent image of mutually interlocked ions is qualitatively correct, even though modifications due to thermal fluctuations are usually strong.Comment: 14 pages, 14 figures, REVTeX4 styl

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is barrierless. A microcanonical analysis, where the energy is the natural variable, has shown better suited to unambiguously characterize the nature of the transition compared to its canonical counterpart. Replica exchange molecular dynamics simulations of a high resolution coarse-grained model allow for the accurate evaluation of the density of states, in order to extract precise thermodynamic information, and measure its impact on structural features. The method is applied to three helical peptides: a short helix shows sharp features of a two-state folder, while a longer helix and a three-helix bundle exhibit downhill and two-state transitions, respectively. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition.Comment: 3 pages, 3 figure

Twist-bend instability for toroidal DNA condensates

We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second structural transition to a twisted entangled state, in which individual filaments lower their bending energy by additionally orbiting around the mean path along which they wind. This ``topological ripening'' is consistent with known simulations and experimental results. It connects and rationalizes various experimental observations ranging from strong DNA entanglement in viral capsids to the unusually short pitch of the cholesteric phase of DNA in sperm-heads. We propose that topological ripening of DNA toroids could improve the efficiency and stability of gene delivery.Comment: 4 pages, 3 figures, RevTeX4 styl

How to mesh up Ewald sums (I): A theoretical and numerical comparison of various particle mesh routines

Standard Ewald sums, which calculate e.g. the electrostatic energy or the force in periodically closed systems of charged particles, can be efficiently speeded up by the use of the Fast Fourier Transformation (FFT). In this article we investigate three algorithms for the FFT-accelerated Ewald sum, which attracted a widespread attention, namely, the so-called particle-particle-particle-mesh (P3M), particle mesh Ewald (PME) and smooth PME method. We present a unified view of the underlying techniques and the various ingredients which comprise those routines. Additionally, we offer detailed accuracy measurements, which shed some light on the influence of several tuning parameters and also show that the existing methods -- although similar in spirit -- exhibit remarkable differences in accuracy. We propose combinations of the individual components, mostly relying on the P3M approach, which we regard as most flexible.Comment: 18 pages, 8 figures included, revtex styl

Efficient tunable generic model for fluid bilayer membranes

We present a model for the efficient simulation of generic bilayer membranes. Individual lipids are represented by one head- and two tail-beads. By means of simple pair potentials these robustly self-assemble to a fluid bilayer state over a wide range of parameters, without the need for an explicit solvent. The model shows the expected elastic behavior on large length scales, and its physical properties (eg fluidity or bending stiffness) can be widely tuned via a single parameter. In particular, bending rigidities in the experimentally relevant range are obtained, at least within $3-30 k_{\text{B}}T$. The model is naturally suited to study many physical topics, including self-assembly, fusion, bilayer melting, lipid mixtures, rafts, and protein-bilayer interactions.Comment: 4 Pages 4 Figure

Overcharging of DNA in the presence of salt: Theory and Simulation

A study of a model rod-like polyelectrolyte molecule immersed into a monovalent or divalent electrolyte is presented. Results from the hypernetted-chain/mean spherical approximation (HNC/MSA) theory, for inhomogeneous charged fluids, {\ch are} compared with molecular dynamics (MD) simulations. As a particular case, the parameters of the polyelectrolyte molecule are mapped to those of a DNA molecule. An excellent qualitative, and in some cases quantitative, agreement between HNC/MSA and MD is found. Both, HNC/MSA and MD, predict the occurrence of overcharging, which is not present in the Poisson-Boltzmann theory. Mean electrostatic potential and local concentration profiles, $\zeta$-potential and charge distribution functions are obtained and discussed in terms of the observed overcharging effect. Particularly interesting results are a very non-monotonic behavior of the $\zeta$-potential, as a function of the rod charge density, and the overcharging by {\em monovalent} counterions.Comment: 11 pages, 8 figures, RevTex, published in J. Phys. Chem. B 2001, vol. 105, pags. 1098