Failure of the work-Hamiltonian connection for free energy calculations

Extensions of statistical mechanics are routinely being used to infer free energies from the work performed over single-molecule nonequilibrium trajectories. A key element of this approach is the ubiquitous expression dW/dt=\partial H(x,t)/ \partial t which connects the microscopic work W performed by a time-dependent force on the coordinate x with the corresponding Hamiltonian H(x,t) at time t. Here we show that this connection, as pivotal as it is, cannot be used to estimate free energy changes. We discuss the implications of this result for single-molecule experiments and atomistic molecular simulations and point out possible avenues to overcome these limitations

Bioautography to assess antibacterial activity of Ottonia martiana Miq. (Piperaceae) on the human oral microbiota.

Ottonia martiana Miq. (Piperaceae), a plant known popularly in southern Brazil as “anestésia” and used in the treatment of odontalgia for its anesthetic action on the oral mucosa, was investigated for antibacterial activity by paper disc agar diffusion and bioautographic methods, against microorganisms present in the human oral cavity [Streptococcus mutans (ATCC 25175), Streptococcus mitis (ATCC 49456), Streptococcus pyogenes (ATCC 19615), Streptococcus salivarius (ATCC 25975), Escherichia coli (ATCC 11229 and 25922), Pseudomonas aeruginosa (ATCC 27853) and Enterobacter aerogenes (ATCC 27853).The crude extract of O. martiana (32.9 mg mL-1) had antibacterial potential against all Gram-positive bacteria tested. Analysis of the bioautograms led to the detection of bioactive substances, among which it was possible to identify piperovatine (Rf 0.35), piperlonguminine (Rf 0.52) and isopiperlonguminine (Rf 0.52). The piperovatine and isopiperlonguminine were isolated from the roots of O. martiana, guided by a bioautographic antibacterial bioassay

1/f1/f noise and avalanche scaling in plastic deformation

We study the intermittency and noise of dislocation systems undergoing shear deformation. Simulations of a simple two-dimensional discrete dislocation dynamics model indicate that the deformation rate exhibits a power spectrum scaling of the type $1/f^{\alpha}$. The noise exponent is far away from a Lorentzian, with $\alpha \approx 1.5$. This result is directly related to the way the durations of avalanches of plastic deformation activity scale with their size.Comment: 6 pages, 5 figures, submitted to Phys. Rev.

On the nonlinear stability of mKdV breathers

A mathematical proof for the stability of mKdV breathers is announced. This proof involves the existence of a nonlinear equation satisfied by all breather profiles, and a new Lyapunov functional which controls the dynamics of small perturbations and instability modes. In order to construct such a functional, we work in a subspace of the energy one. However, our proof introduces new ideas in order to attack the corresponding stability problem in the energy space. Some remarks about the sine-Gordon case are also considered.Comment: 7 p

Self-Pulsating Semiconductor Lasers: Theory and Experiment

We report detailed measurements of the pump-current dependency of the self-pulsating frequency of semiconductor CD lasers. A distinct kink in this dependence is found and explained using rate-equation model. The kink denotes a transition between a region where the self-pulsations are weakly sustained relaxation oscillations and a region where Q-switching takes place. Simulations show that spontaneous emission noise plays a crucial role for the cross-over.Comment: Revtex, 16 pages, 7 figure

Avaliação do real potencial inibidor de extratos etanólicos de Ottonia martiana sobre Cylindrocladium spathulatum e Botrytis cinerea.

Extratos etanólicos de anestesia, Ottonia martiana Miq., foram reavaliados quanto à inibição do crescimento micelial dos fungos Cylindrocladium spathulatum (pinta-preta da erva-mate) e Botrytis cinerea (mofo-cinzento do eucalipto), por meio do planejamento fatorial. A ocorrência de decomposição de bioativos no processo de autoclavagem também foi investigada, por meio de teste de eficiência de extratos filtrados (filtro Millipore) e esterilizados (autoclave) no controle dos fitopatógenos, nas concentrações de 1, 10, 100 e 1000 ppm. Os extratos etanólicos filtrado e esterilizado inibiram o crescimento micelial dos fungos e foram mais ativos frente a B. cinerea. O extrato filtrado exibiu maior potencial antifúngico que o extrato esterilizado. O processo de esterilização por autoclavagem causou pequena decomposição dos bioativos presentes no extrato de anestesia

Sharp error terms for return time statistics under mixing conditions

We describe the statistics of repetition times of a string of symbols in a stochastic process. Denote by T(A) the time elapsed until the process spells the finite string A and by S(A) the number of consecutive repetitions of A. We prove that, if the length of the string grows unbondedly, (1) the distribution of T(A), when the process starts with A, is well aproximated by a certain mixture of the point measure at the origin and an exponential law, and (2) S(A) is approximately geometrically distributed. We provide sharp error terms for each of these approximations. The errors we obtain are point-wise and allow to get also approximations for all the moments of T(A) and S(A). To obtain (1) we assume that the process is phi-mixing while to obtain (2) we assume the convergence of certain contidional probabilities

Polyion Adsorption onto Catanionic Surfaces. A Monte Carlo Study

The adsorption of a single and negatively charged polyion with varying flexibility onto a surface carrying both negative and positive charges representing a charged membrane surface has been investigated by using a simple model employing Monte Carlo simulations. The polyion was represented by a sequence of negatively charged hard spheres connected with harmonic bonds. The charged surface groups were also represented by charged hard spheres, and they were positioned on a hard surface slightly protruding into the solution. The surface charges were either frozen in a liquidlike structure or laterally mobile. With a large excess of positive surface charges, the classical picture of a strongly adsorbed polyion with an extended and flat configuration emerged. However, adsorption also appeared at a net neutral surface or at a weakly negatively charged surface, and at these conditions the adsorption was stronger with a flexible polyion as compared to a semiflexible one, two features not appearing in simpler models containing homogeneously charged surfaces. The presence of charged surface patches (frozen surface charges) and the ability of polarization of the surface charges (mobile surface charges) are the main reasons for the enhanced adsorption. The stronger adsorption with the flexible chain is caused by its greater ability to spatially correlate with the surface charges

First order phase transition in a nonequilibrium growth process

We introduce a simple continuous model for nonequilibrium surface growth. The dynamics of the system is defined by the KPZ equation with a Morse-like potential representing a short range interaction between the surface and the substrate. The mean field solution displays a non trivial phase diagram with a first order transition between a growing and a bound surface, associated with a region of coexisting phases, and a tricritical point where the transition becomes second order. Numerical simulations in 3 dimensions show quantitative agreement with mean field results, and the features of the phase space are preserved even in 2 dimensions.Comment: 7 figures, revtex, submitted to Phys. Rev.