Breathers and Thermal Relaxation in Fermi-Pasta-Ulam Arrays

Breather stability and longevity in thermally relaxing nonlinear arrays depend sensitively on their interactions with other excitations. We review the relaxation of breathers in Fermi-Pasta-Ulam arrays, with a specific focus on the different relaxation channels and their dependence on the interparticle interactions, dimensionality, initial condition, and system parameters

Generation of dynamic structures in nonequilibrium reactive bilayers

We present a nonequlibrium approach for the study of a flexible bilayer whose two components induce distinct curvatures. In turn, the two components are interconverted by an externally promoted reaction. Phase separation of the two species in the surface results in the growth of domains characterized by different local composition and curvature modulations. This domain growth is limited by the effective mixing due to the interconversion reaction, leading to a finite characteristic domain size. In addition to these effects, first introduced in our earlier work [Phys. Rev. E {\bf 71}, 051906 (2005)], the important new feature is the assumption that the reactive process actively affects the local curvature of the bilayer. Specifically, we suggest that a force energetically activated by external sources causes a modification of the shape of the membrane at the reaction site. Our results show the appearance of a rich and robust dynamical phenomenology that includes the generation of traveling and/or oscillatory patterns. Linear stability analysis, amplitude equations and numerical simulations of the model kinetic equations confirm the occurrence of these spatiotemporal behaviors in nonequilibrium reactive bilayers.Comment: To appear in Phys. Rev.

Effects of some mixing flows on diffusion-controlled reactions = Efectes d'alguns fluxes de mescla en reaccions controlades per difusió

[spa] Los sistemas de reacción-difusión donde el proceso difusivo es la etapa lenta están controlados, a bajas dimensionalidades, por las fluctuaciones en las distribuciones iniciales de reactivos. Concretamente, estos sistemas se segregan en dominios de las diferentes especies obteniéndose comportamientos cinéticos anómalos. Estudiamos estos comportamientos no formales en el sistema reactivo binario A+B=O mediante la explotación analítica y numérica de las ecuaciones deterministas de reacción-difusión para las concentraciones locales de ambos reactivos suponiendo válida la aproximación de campo medio para el término de reacción. En una segunda parte del trabajo se ha incorporado al modelo un tercer proceso, el de mezcla, con el que intentamos homogeneizar el sistema y recuperar el comportamiento cinético clásico. Trabajamos principalmente con dos flujos hidrodinámicos bidimensionales, el de red de remolinos y el turbulento. Si bien en ambos casos a tiempos intermedios recuperamos la conducta clásica, a tiempos suficientemente grandes conseguimos evitar la segregación del sistema

Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia

The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic) and carbon tetrachloride (non-anesthetic). Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action

On the Generalized Kramers Problem with Oscillatory Memory Friction

The time-dependent transmission coefficient for the Kramers problem exhibits different behaviors in different parameter regimes. In the high friction regime it decays monotonically ("non-adiabatic"), and in the low friction regime it decays in an oscillatory fashion ("energy-diffusion-limited"). The generalized Kramers problem with an exponential memory friction exhibits an additional oscillatory behavior in the high friction regime ("caging"). In this paper we consider an oscillatory memory kernel, which can be associated with a model in which the reaction coordinate is linearly coupled to a nonreactive coordinate, which is in turn coupled to a heat bath. We recover the non-adiabatic and energy-diffusion-limited behaviors of the transmission coefficient in appropriate parameter regimes, and find that caging is not observed with an oscillatory memory kernel. Most interestingly, we identify a new regime in which the time-dependent transmission coefficient decays via a series of rather sharp steps followed by plateaus ("stair-like"). We explain this regime and its dependence on the various parameters of the system

Effects of Dimethyl Sulfoxide on Lipid Membrane Electroporation

Pores can be generated in lipid membranes by the application of an external electric field or by the addition of particular chemicals such as dimethyl sulfoxide (DMSO). Molecular dynamics (MD) has been shown to be a useful tool for unveiling many aspects of pore formation in lipid membranes in both situations. By means of MD simulations, we address the formation of electropores in cholesterol-containing lipid bilayers under the influence of DMSO. We show how a combination of physical and chemical mechanisms leads to more favorable conditions for generating membrane pores and, in particular, how the addition of DMSO to the medium significantly reduces the minimum electric field required to electroporate a lipid membrane. The strong alteration of membrane transversal properties and the energetic stabilization of the hydrophobic pore stage by DMSO provide the physicochemical mechanisms that explain this effec

Effects of fullerene on lipid bilayers displaying different liquid ordering: a coarse-grained molecular dynamics study

Background The toxic effects and environmental impact of nanomaterials, and in particular of Fullerene particles, are matters of serious concern. It has been reported that fullerene molecules enter the cell membrane and occupy its hydrophobic region. Understanding the effects of Carbon-based nanoparticles on biological membranes is therefore of critical importance to determine their exposure risks. Methods We report on a systematic coarse-grained molecular dynamics study of the interaction of fullerene molecules with simple model cell membranes. We have analyzed bilayers consisting of lipid species with different degrees of unsaturation and a variety of cholesterol fractions. Addition of fullerene particles to phase-segregated ternary membranes is also investigated in the context of the lipid raft model for the organization of the cell membrane. Results Fullerene addition to lipid membranes modifies their structural properties like thickness, area and internal ordering of the lipid species, as well as dynamical aspects such as molecular diffusion and cholesterol flip-flop. Interestingly, we show that phase-segregating ternary lipid membranes accumulate fullerene molecules preferentially in the liquid-disordered domains promoting phase-segregation and domain alignment across the membrane. Conclusions Lipid membrane internal ordering determines the behavior and distribution of fullerene particle, and this, in turn, determines the influence of fullerene on the membrane. Lipid membranes are good solvents of fullerene molecules, and in particular those with low internal ordering. General Significance Preference of fullerene molecules to be dissolved in the more disordered hydrophobic regions of a lipid bilayer and the consequent alteration of its phase behavior may have important consequences on the activity of biological cell membranes and on the bioconcentration of fullerene in living organisms.Peer ReviewedPostprint (author's final draft

Interaction modes between nanosized grapheneflakes and liposomes: adsorption, insertion and membrane fusion

Background: Understanding the effects of graphene-based nanomaterials on lipid membranes is critical to determine their environmental impact and their efficiency in the biomedical context. Graphene has been reported to favourably interact with biological and model lipid membranes. Methods: We report on a systematic coarse-grained molecular dynamics study of the interaction modes of graphene nanometric flakes with POPC/cholesterol liposome membranes. We have simulated graphene layers with a variety of sizes and oxidation degrees, and we have analyzed the trajectories, the interaction modes, and the energetics of the observed phenomena.Results:Three interaction modes are reported. Graphene can be transiently adsorbed onto the liposome membrane and/or inserted in its hydrophobic region. Inserted nanosheets prefer a perpendicular orientation, and tilt in order to maximize the contact with phospholipid tails while avoiding the contact with cholesterol molecules.When placed between two liposomes, graphene facilitates their fusion in a single vesicle. Conclusions: Graphene can be temporary adsorbed on the liposome before insertion. Bilayer curvature has an influence on the orientation of inserted graphene particles. Cholesterol molecules are depleted from the surrounding of graphene particles. Graphene layers may catalyse membrane fusion by bypassing the energy barrier required in stalk formation. General significance: Nanometric graphene layers can be adsorbed/inserted in lipid-based membranes in different manners and affect the cholesterol distribution in the membrane, implying important consequences on the structure and functionality of biological cell membranes, and on the bioaccumulation of graphene in living organisms. The graphene-mediated mechanism opens new possibilities for vesicle fusion in the experimental context