Ard A. Louis

Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length scales

We describe in detail how to implement a coarse-grained hybrid molecular dynamics and stochastic rotation dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The importance of carefully tuning the simulation parameters to correctly resolve the multiple time and length scales of this problem is emphasized. We systematically analyze how our coarse-graining scheme resolves dimensionless hydrodynamic numbers such as the Reynolds number Re, which indicates the importance of inertial effects, the Schmidt number Sc, which indicates whether momentum transport is liquidlike or gaslike, the Mach number, which measures compressibility effects, the Knudsen number, which describes the importance of noncontinuum molecular effects, and the Peclet number, which describes the relative effects of convective and diffusive transport. With these dimensionless numbers in the correct regime the many Brownian and hydrodynamic time scales can be telescoped together to maximize computational efficiency while still correctly resolving the physically relevant processes. We also show how to control a number of numerical artifacts, such as finite-size effects and solvent-induced attractive depletion interactions. When all these considerations are properly taken into account, the measured colloidal velocity autocorrelation functions and related self-diffusion and friction coefficients compare quantitatively with theoretical calculations. By contrast, these calculations demonstrate that, notwithstanding its seductive simplicity, the basic Langevin equation does a remarkably poor job of capturing the decay rate of the velocity autocorrelation function in the colloidal regime, strongly underestimating it at short times and strongly overestimating it at long times. Finally, we discuss in detail how to map the parameters of our method onto physical systems and from this extract more general lessons-keeping in mind that there is no such thing as a free lunch-that may be relevant for other coarse-graining schemes such as lattice Boltzmann or dissipative particle dynamics.

Beware of density dependent pair potentials

Density (or state) dependent pair potentials arise naturally from coarse-graining procedures in many areas of condensed matter science. However, correctly using them to calculate physical properties of interest is subtle and cannot be uncoupled from the route by which they were derived. Furthermore, there is usually no unique way to coarse-grain to an effective pair potential. Even for simple systems like liquid argon, the pair potential that correctly reproduces the pair structure will not generate the right virial pressure. Ignoring these issues in naive applications of density dependent pair potentials can lead to an apparent dependence of thermodynamic properties on the ensemble within which they are calculated, as well as other inconsistencies. These concepts are illustrated by several pedagogical examples, including effective pair potentials for systems with many-body interactions, and the mapping of charged (Debye–Huckel) and uncharged (Asakura–Oosawa) two-component systems onto effective one-component ones. The differences between the problems of transferability and representability for effective potentials are also discussed.

Accurate Effective Pair Potentials for Polymer Solutions

Dilute or semidilute solutions of nonintersecting self-avoiding walk (SAW) polymer chains are mapped onto a fluid of “soft” particles interacting via an effective pair potential between their centers of mass. This mapping is achieved by inverting the pair distribution function of the centers of mass of the original polymer chains, using integral equation techniques from the theory of simple fluids. The resulting effective pair potential is finite at all distances, has a range of the order of the radius of gyration, and turns out to be only moderately concentration-dependent. The dependence of the effective potential on polymer length is analyzed in an effort to extract the scaling limit. The effective potential is used to derive the osmotic equation of state, which is compared to simulation data for the full SAW segment model, and to the predictions of renormalization group calculations. A similar inversion procedure is used to derive an effective wall–polymer potential from the center of mass density pro...

On the Biophysics and Kinetics of Toehold-Mediated DNA Strand Displacement

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

Representability problems for coarse-grained water potentials.

The use of an effective intermolecular potential often involves a compromise between more accurate, complex functional forms and more tractable simple representations. To study this choice in detail, we systematically derive coarse-grained isotropic pair potentials that accurately reproduce the oxygen-oxygen radial distribution function of the TIP4P-Ew water model at state points over density ranges from 0.88 to 1.30 g/cm3 and temperature ranges from 235 to 310 K. Although by construction these effective potentials correctly represent the isothermal compressibility of TIP4P-Ew water, they do not accurately resolve other thermodynamic properties such as the virial pressure, the internal energy, or thermodynamic anomalies. Because at a given state point the pair potential that reproduces the pair structure is unique, we have therefore explicitly demonstrated that it is impossible to simultaneously represent the pair structure and several key equilibrium thermodynamic properties of water with state-point dependent radially symmetric pair potentials. We argue that such representability problems are related to, but different from, more widely acknowledged transferability problems and discuss in detail the implications this has for the modeling of water and other liquids by coarse-grained potentials. Nevertheless, regardless of thermodynamic inconsistencies, the state-point dependent effective potentials for water do generate structural and dynamical anomalies.

Influence of Polymer-Excluded Volume on the Phase-Behavior of Colloid-Polymer Mixtures

We determine the depletion-induced phase-behavior of hard-sphere colloids and interacting polymers by large-scale Monte Carlo simulations using very accurate coarse-graining techniques. A comparison with standard Asakura-Oosawa model theories and simulations shows that including excluded-volume interactions between polymers leads to qualitative differences in the phase diagrams. These effects become increasingly important for larger relative polymer size. Our simulation results agree quantitatively with recent experiments.

Reversible self-assembly of patchy particles into monodisperse icosahedral clusters

We systematically study the design of simple patchy sphere models that reversibly self-assemble into monodisperse icosahedral clusters. We find that the optimal patch width is a compromise between structural specificity (the patches must be narrow enough to energetically select the desired clusters) and kinetic accessibility (they must be sufficiently wide to avoid kinetic traps). Similarly, for good yields the temperature must be low enough for the clusters to be thermodynamically stable, but the clusters must also have enough thermal energy to allow incorrectly formed bonds to be broken. Ordered clusters can form through a number of different dynamic pathways, including direct nucleation and indirect pathways involving large disordered intermediates. The latter pathway is related to a reentrant liquid-to-gas transition that occurs for intermediate patch widths upon lowering the temperature. We also find that the assembly process is robust to inaccurate patch placement up to a certain threshold and that it is possible to replace the five discrete patches with a single ring patch with no significant loss in yield.

Sequence-dependent thermodynamics of a coarse-grained DNA model

We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software.

Polymer induced depletion potentials in polymer-colloid mixtures

The depletion interactions between two colloidal plates or between two colloidal spheres, induced by interacting polymers in a good solvent, are calculated theoretically and by computer simulations. A simple analytical theory is shown to be quantitatively accurate for the case of two plates. A related depletion potential is derived for two spheres; it also agrees very well with direct computer simulations. Theories based on ideal polymers show important deviations with increasing polymer concentration: They overestimate the range of the depletion potential between two plates or two spheres at all densities, with the largest relative change occurring in the dilute regime. They underestimate the well depth at contact for the case of two plates, but overestimate it for two spheres. Depletion potentials are also calculated using a coarse graining approach which represents the polymers as “soft colloids;” good agreement is found in the dilute regime. Finally, the effect of the polymers on colloid–colloid osmot...

Hydrodynamic and Brownian Fluctuations in Sedimenting Suspensions

We use a mesoscopic computer simulation method to study the interplay between hydrodynamic and Brownian fluctuations during steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.1-15. Even when the hydrodynamic interactions are an order of magnitude weaker than Brownian forces, they still induce backflow effects that dominate the reduction of the average sedimentation velocity with increasing particle packing fraction. Velocity fluctuations, on the other hand, begin to show nonequilibrium hydrodynamic character for Pe>1.