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

Folding and insertion thermodynamics of the transmembrane WALP peptide

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)$_n$(L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum---in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.Comment: 12 pages, 5 figure

Spectral representation of the effective dielectric constant of graded composites

We generalize the Bergman-Milton spectral representation, originally derived for a two-component composite, to extract the spectral density function for the effective dielectric constant of a graded composite. This work has been motivated by a recent study of the optical absorption spectrum of a graded metallic film [Applied Physics Letters, 85, 94 (2004)] in which a broad surface-plasmon absorption band has been shown to be responsible for enhanced nonlinear optical response as well as an attractive figure of merit. It turns out that, unlike in the case of homogeneous constituent components, the characteristic function of a graded composite is a continuous function because of the continuous variation of the dielectric function within the constituent components. Analytic generalization to three dimensional graded composites is discussed, and numerical calculations of multilayered composites are given as a simple application.Comment: Physical Review E, submitted for publication

Integration Schemes for Dissipative Particle Dynamics Simulations: From Softly Interacting Systems Towards Hybrid Models

We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often studied in simulations. Specifically we clarify the performance of integration schemes in hybrid models, which combine microscopic and meso-scale descriptions of different particles using both soft and hard interactions. We find that in all three model systems many commonly used integrators may give rise to surprisingly pronounced artifacts in physical observables such as the radial distribution function, the compressibility, and the tracer diffusion coefficient. The artifacts are found to be strongest in systems, where interparticle interactions are soft and predominated by random and dissipative forces, while in systems governed by conservative interactions the artifacts are weaker. Our results suggest that the quality of any integration scheme employed is crucial in all cases where the role of random and dissipative forces is important, including hybrid models where the solvent is described in terms of soft potentials

Enhanced dielectrophoresis of nanocolloids by dimer formation

We investigate the dielectrophoretic motion of charge-neutral, polarizable nanocolloids through molecular dynamics simulations. Comparison to analytical results derived for continuum systems shows that the discrete charge distributions on the nanocolloids have a significant impact on their coupling to the external field. Aggregation of nanocolloids leads to enhanced dielectrophoretic transport, provided that increase in the dipole moment upon aggregation can overcome the related increase in friction. The dimer orientation and the exact structure of the nanocolloid charge distribution are shown to be important in the enhanced transport

KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability.

We have performed 280 μs of unbiased molecular dynamics (MD) simulations to investigate the effects of 12 different cancer mutations on Kelch-like ECH-associated protein 1 (KEAP1) (G333C, G350S, G364C, G379D, R413L, R415G, A427V, G430C, R470C, R470H, R470S and G476R), one of the frequently mutated proteins in lung cancer. The aim was to provide structural insight into the effects of these mutants, including a new class of ANCHOR (additionally NRF2-complexed hypomorph) mutant variants. Our work provides additional insight into the structural dynamics of mutants that could not be analyzed experimentally, painting a more complete picture of their mutagenic effects. Notably, blade-wise analysis of the Kelch domain points to stability as a possible target of cancer in KEAP1. Interestingly, structural analysis of the R470C ANCHOR mutant, the most prevalent missense mutation in KEAP1, revealed no significant change in structural stability or NRF2 binding site dynamics, possibly indicating an covalent modification as this mutant\u27s mode of action

Nutrient and energy potential for sustainable biorefineries based on wastes of agrifood systems: two regional cases

The aim of our study is to identify business models and opportunities with corporate social responsibility(CSR) presented by biorefineries based on wastes and return flows of agrifood systems. Two regional cases are explored and methods for generalisation are developed