From simple surface models to lipid membranes: Universal aspects of the hydration interaction from solvent-explicit simulations

A review of atomistic simulation approaches including explicit water for the study of hydration forces between polar surfaces is presented. In particular, we discuss different methods for keeping the chemical potential of water constant and compare advantages and limitations of each method. It turns out that modifications of hydration forces due to surface softness can be accounted for by a convolution over the surface shape profile. Universal aspects of the hydration interaction observed in simulations of different surface chemistries are highlighted, while special attention is given to hydration forces between self-assembled phospholipid membranes.     

Electrostatistics of counter-ions at and between planar charged walls: From Poisson-Boltzmann to the strong-coupling theory

The European Physical Journal E - The Poisson-Boltzmann (PB) approach gives asymptotically exact counter-ion density profiles around macroscopic charged objects and forces between macroscopic...     

End-monomer Dynamics in Semiflexible Polymers

Spurred by an experimental controversy in the literature, we investigate the end-monomer dynamics of semiflexible polymers through Brownian hydrodynamic simulations and dynamic mean-field theory. Precise experimental observations over the last few years of end-monomer dynamics in the diffusion of double-stranded DNA have given conflicting results: one study indicated an unexpected Rouse-like scaling of the mean squared displacement (MSD) ?r(2)(t)? ~ t(1/2) at intermediate times, corresponding to fluctuations at length scales larger than the persistence length but smaller than the coil size; another study claimed the more conventional Zimm scaling ?r(2)(t)? ~ t(2/3) in the same time range. Using hydrodynamic simulations, analytical and scaling theories, we find a novel intermediate dynamical regime where the effective local exponent of the end-monomer MSD, α(t) = d log?r(2)(t)?/d log t, drops below the Zimm value of 2/3 for sufficiently long chains. The deviation from the Zimm prediction increases with chain length, though it does not reach the Rouse limit of 1/2. The qualitative features of this intermediate regime, found in simulations and in an improved mean-field theory for semiflexible polymers, in particular the variation of α(t) with chain and persistence lengths, can be reproduced through a heuristic scaling argument. Anomalously low values of the effective exponent α are explained by hydrodynamic effects related to the slow crossover from dynamics on length scales smaller than the persistence length to dynamics on larger length scales.     

Time-dependent electric quadrupole interactions in (NH4)3HfF7

Spinrotation spectra of polycrystalline (NH₄)₃HfF₇ in which radioactive¹⁸¹Hf was incorporated have been measured in the temperature range from ?196 °C to + 70 °C. The spectra were interpretated on the base of the stochastic model of M. Blume. It was assumed that reorientations of the [HfF₇]^3? polyhedra take place at random. The resulting fluctuation rates can be understood as to be caused by an activation process. The activation energy was determined to 0.324(12) eV in agreement with NMR measurements on¹⁹F in this compound.     

The quadrupole moment of the 535 keV state of 133La

The quadrupole moment of the 535 keV $\text{3}\text{2}{}^{\mathrm{?}}$ state of ¹³³La has been derived from a time-differential perturbed angular correlation measurement in an environment of La metal. The effective electric gradient is known from a nuclear quadrupole resonance measurement with the ground state of ¹³⁹La. The result Q = 0.35 ± 0.03 b does not confirm a proposed shape isomerism.     

Impact of loop statistics on the thermodynamics of RNA folding

Loops are abundant in native RNA structures and proliferate close to the unfolding transition. By including a statistical weight approximately l(-c) for loops of length l in the recursion relation for the partition function, we show that the heat capacity depends sensitively on the presence and value of the exponent c, even for a short explicit tRNA sequence. For long homo-RNA, we analytically calculate the critical temperature and critical exponents which exhibit a nonuniversal dependence on c.     

Model for self-propulsive helical filaments: kink-pair propagation

Spiroplasma bacteria propel through viscous fluids by sending kinks or domain walls between regions of opposite handedness down their helical body. A simple elastic model for the domain-wall propagation is formulated and studied using hydrodynamic simulations and scaling arguments, giving good agreement with recent video-microscopy observations. It is shown that the observed helical bacterial pitch angle psi approximately 35 degrees is optimized for maximal speed and efficiency.     

Anomalous polymer sedimentation far from equilibrium

A single flexible polymer in strong sedimentation fields is investigated using hydrodynamic simulations and scaling arguments. For short chains and small fields compaction is observed. For elevated fields or long chains the chain stretches and the sedimentation coefficient decreases, in agreement with ultracentrifuge experiments on linear as well as circular DNA. For very large fields a tadpole forms consisting of a compact leading head and a trailing stretched tail.     

Ionic force field optimization based on single-ion and ion-pair solvation properties: going beyond standard mixing rules

Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single-ion solvation free energies, and in a second step determine the cation-anion interaction parameters (traditionally given by mixing or combination rules) based on the Kirkwood-Buff theory without modification of the ion-water interaction parameters. In doing so, we have introduced scaling factors for the cation-anion Lennard-Jones (LJ) interaction that quantify deviations from the standard mixing rules. For the rather size-symmetric salt solutions involving bromide and chloride ions, the standard mixing rules work fine. On the other hand, for the iodide and fluoride solutions, corresponding to the largest and smallest anion considered in this work, a rescaling of the mixing rules was necessary. For iodide, the experimental activities suggest more tightly bound ion pairing than given by the standard mixing rules, which is achieved in simulations by reducing the scaling factor of the cation-anion LJ energy. For fluoride, the situation is different and the simulations show too large attraction between fluoride and cations when compared with experimental data. For NaF, the situation can be rectified by increasing the cation-anion LJ energy. For KF, it proves necessary to increase the effective cation-anion Lennard-Jones diameter. The optimization strategy outlined in this work can be easily adapted to different kinds of ions.