Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration and structural properties

In this paper we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium and, to a lesser extent, chloride translate into large differences in the computed radial-distribution functions. This uncertainty reflects the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity.We discuss possible implications on the computation of potential of mean force and effective potentials.Comment: Revised and extended manuscrip

Multiphase density functional theory parameterization of the Gupta potential for silver and gold

The ground state energies of Ag and Au in the face-centered cubic (FCC), body-centered cubic (BCC), simple cubic (SC) and the hypothetical diamond-like phase, and dimer were calculated as a function of bond length using density functional theory (DFT). These energies were then used to parameterize the many-body Gupta potential for Ag and Au. This parameterization over several phases of Ag and Au was performed to guarantee transferability of the potentials and to make them appropriate for studies of related nanostructures. Depending on the structure, the energetics of the surface atoms play a crucial role in determining the details of the nanostructure. The accuracy of the parameters was tested by performing a 2 ns MD simulation of a cluster of 55 Ag atoms -- a well studied cluster of Ag, the most stable structure being the icosahedral one. Within this time scale, the initial FCC lattice was found to transform to the icosahedral structure at room temperature. The new set of parameters for Ag was then used in a temperature dependent atom-by-atom deposition of Ag nanoclusters of up to 1000 atoms. We find a deposition temperature of 500 $\pm$50 K where low energy clusters are generated, suggesting an optimal annealing temperature of 500 K for Ag cluster synthesis

Stability of charge inversion, Thomson problem and application to electrophoresis

We analyse charge inversion in colloidal systems at zero temperature using stability concepts, and connect this to the classical Thomson problem of arranging electrons on sphere. We show that for a finite microion charge, the globally stable, lowest energy state of the complex formed by the colloid and the oppositely charged microions is always overcharged. This effect disappears in the continuous limit. Additionally, a layer of at least twice as many microions as required for charge neutrality is always locally stable. In an applied external electric field the stability of the microion cloud is reduced. Finally, this approach is applied to a system of two colloids at low but finite temperature

Getting excited: Challenges in quantum-classical studies of excitons in polymeric systems

A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) was performed to describe conformational properties of diphenylethyne (DPE), methylated-DPE and poly para phenylene ethynylene (PPE). DFT calculations were employed to improve and develop force field parameters for MM/MD simulations. Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation were utilized to describe excited states of the systems. Reliability of the excitation energies based on the MM/MD conformations was examined and compared to the excitation energies from DFT conformations. The results show an overall agreement between the optical excitations based on MM/MD conformations and DFT conformations. This allows for calculation of excitation energies based on MM/MD conformations

Micelle fragmentation and wetting in confined flow

We use coarse-grained molecular-dynamics (MD) simulations to investigate the structural and dynamical properties of micelles under non-equilibrium Poiseuille flow in a nano-confined geometry. The effects of flow, confinement, and the wetting properties of die-channel walls on spherical sodium dodecyl sulfate (SDS) micelles are explored when the micelle is forced through a die-channel slightly smaller than its equilibrium size. Inside the channel, the micelle may fragment into smaller micelles. In addition to the flow rate, the wettability of the channel surfaces dictates whether the micelle fragments and determines the size of the daughter micelles: The overall behavior is determined by the subtle balance between hydrodynamic forces, micelle-wall interactions and self-assembly forces

Crumpling of a stiff tethered membrane

first-principles numerical simulation model for crumpling of a stiff tethered membrane is introduced. In our model membranes, wrinkles, ridge formation, ridge collapse, as well as the initiation of stiffness divergence, are observed. The ratio of the amplitude and wave length of the wrinkles, and the scaling exponent of the stiffness divergence, are consistent with both theory and experiment. We observe that close to the stiffness divergence there appears a crossover beyond which the elastic behavior of a tethered membrane becomes similar to that of dry granular media. This suggests that ridge formation in membranes and force-chain network formation in granular packings are different manifestations of a single phenomenon.Comment: For full resolution figures, please send us an emai

Morphology of Proliferating Epithelial Cellular Tissue

We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective division and division plane orientation. The model is applied to a bimodal mixture of stiff cells with a low growth potential and soft cells with a high growth potential. In an even mixture, the soft cells develop into a tissue matrix and the stiff cells into a dendrite-like network structure. For soft cell inclusion in a stiff cellular matrix, the soft cells develop to a fast growing tumour like structure that gradually evacuates the stiff cell matrix. With increasing inter-cell friction, the tumour growth slows down and parts of it is driven to self-inflicted cell death

Using Molecular Dynamics to Study QS21 Interactions and Penetration of Lipid-Cholesterol Bilayers

Saponins have been used as adjuvant agents for decades in vaccines and therapies, but none are as well studied or heavily used as QS-21. This achievement is notwithstanding the fact that QS-21 usage is limited by its stability, toxicity, and scarcity. These shortcomings have only pushed researchers to develop and experiment with artificial recreations of the saponin to harness its unique benefits. A considerable number of research hours have been poured into this topic, but like QS-21 there is a shortcoming here as well. The number of articles that look at QS-21 interactions with the bilayer or the conditions under which QS-21 will interact appeared as scarcely as QS-21 itself. In this work, we used molecular dynamic simulations to study how QS-21 interacts with the plasma membrane also known as the cell bilayer. To gain a proper understanding of the interactions, we created multiple systems designed to address a certain set of questions. Most of these systems are large lipid-cholesterol systems made from dipalmitoyl-phosphatidylcholine (DPPC), dioleoyl-phosphatidylcholine (DOPC), or distearoyl-phosphatidylcholine (DSPC) mixed with cholesterol with differing numbers of QS-21 molecules to investigate how the saponin interacts with the bilayer. Others were reference systems of QS-21 and counterions to understand QS-21 self-interactions. Lastly, some where designed for free energy difference calculations to quantify which bilayer composition was most favourable. We aim to provide an atomic-level understanding of QS-21 and bilayer interactions that can be used by experimentalists and theoreticians to develop better ways of studying QS-21 themselves by combining these results together

Nucleation, growth, and scaling in slow combustion

We study the nucleation and growth of flame fronts in slow combustion. This is modeled by a set of reaction-diffusion equations for the temperature field, coupled to a background of reactants and augmented by a term describing random temperature fluctuations for ignition. We establish connections between this model and the classical theories of nucleation and growth of droplets from a metastable phase. Our results are in good argeement with theoretical predictions.Comment: RevTeX+epsf macros, 6 pages, 6 figure