Non-equilibrium dynamics of stochastic point processes with refractoriness

Stochastic point processes with refractoriness appear frequently in the quantitative analysis of physical and biological systems, such as the generation of action potentials by nerve cells, the release and reuptake of vesicles at a synapse, and the counting of particles by detector devices. Here we present an extension of renewal theory to describe ensembles of point processes with time varying input. This is made possible by a representation in terms of occupation numbers of two states: Active and refractory. The dynamics of these occupation numbers follows a distributed delay differential equation. In particular, our theory enables us to uncover the effect of refractoriness on the time-dependent rate of an ensemble of encoding point processes in response to modulation of the input. We present exact solutions that demonstrate generic features, such as stochastic transients and oscillations in the step response as well as resonances, phase jumps and frequency doubling in the transfer of periodic signals. We show that a large class of renewal processes can indeed be regarded as special cases of the model we analyze. Hence our approach represents a widely applicable framework to define and analyze non-stationary renewal processes.Comment: 8 pages, 4 figure

(Quantum) Space-Time as a Statistical Geometry of Fuzzy Lumps and the Connection with Random Metric Spaces

We develop a kind of pregeometry consisting of a web of overlapping fuzzy lumps which interact with each other. The individual lumps are understood as certain closely entangled subgraphs (cliques) in a dynamically evolving network which, in a certain approximation, can be visualized as a time-dependent random graph. This strand of ideas is merged with another one, deriving from ideas, developed some time ago by Menger et al, that is, the concept of probabilistic- or random metric spaces, representing a natural extension of the metrical continuum into a more microscopic regime. It is our general goal to find a better adapted geometric environment for the description of microphysics. In this sense one may it also view as a dynamical randomisation of the causal-set framework developed by e.g. Sorkin et al. In doing this we incorporate, as a perhaps new aspect, various concepts from fuzzy set theory.Comment: 25 pages, Latex, no figures, some references added, some minor changes added relating to previous wor

Scaling-violation phenomena and fractality in the human posture control systems

By analyzing the movements of quiet standing persons by means of wavelet statistics, we observe multiple scaling regions in the underlying body dynamics. The use of the wavelet-variance function opens the possibility to relate scaling violations to different modes of posture control. We show that scaling behavior becomes close to perfect, when correctional movements are dominated by the vestibular system.Comment: 12 pages, 4 figures, to appear in Phys. Rev.

Liquid-liquid equilibrium for monodisperse spherical particles

A system of identical particles interacting through an isotropic potential that allows for two preferred interparticle distances is numerically studied. When the parameters of the interaction potential are adequately chosen, the system exhibits coexistence between two different liquid phases (in addition to the usual liquid-gas coexistence). It is shown that this coexistence can occur at equilibrium, namely, in the region where the liquid is thermodynamically stable.Comment: 6 pages, 8 figures. Published versio

Point-occurrence self-similarity in crackling-noise systems and in other complex systems

It has been recently found that a number of systems displaying crackling noise also show a remarkable behavior regarding the temporal occurrence of successive events versus their size: a scaling law for the probability distributions of waiting times as a function of a minimum size is fulfilled, signaling the existence on those systems of self-similarity in time-size. This property is also present in some non-crackling systems. Here, the uncommon character of the scaling law is illustrated with simple marked renewal processes, built by definition with no correlations. Whereas processes with a finite mean waiting time do not fulfill a scaling law in general and tend towards a Poisson process in the limit of very high sizes, processes without a finite mean tend to another class of distributions, characterized by double power-law waiting-time densities. This is somehow reminiscent of the generalized central limit theorem. A model with short-range correlations is not able to escape from the attraction of those limit distributions. A discussion on open problems in the modeling of these properties is provided.Comment: Submitted to J. Stat. Mech. for the proceedings of UPON 2008 (Lyon), topic: crackling nois

A novel HLA-B18 restricted CD8+ T cell epitope is efficiently cross-presented by dendritic cells from soluble tumor antigen

NY-ESO-1 has been a major target of many immunotherapy trials because it is expressed by various cancers and is highly immunogenic. In this study, we have identified a novel HLA-B*1801-restricted CD8<sup>+</sup>T cell epitope, NY-ESO-1<sub>88–96</sub> (LEFYLAMPF) and compared its direct- and cross-presentation to that of the reported NY-ESO-1<sub>157–165</sub> epitope restricted to HLA-A*0201. Although both epitopes were readily cross-presented by DCs exposed to various forms of full-length NY-ESO-1 antigen, remarkably NY-ESO-1<sub>88–96</sub> is much more efficiently cross-presented from the soluble form, than NY-ESO-1<sub>157–165</sub>. On the other hand, NY-ESO-1<sub>157–165</sub> is efficiently presented by NY-ESO-1-expressing tumor cells and its presentation was not enhanced by IFN-γ treatment, which induced immunoproteasome as demonstrated by Western blots and functionally a decreased presentation of Melan A<sub>26–35</sub>; whereas NY-ESO-1<sub>88–96</sub> was very inefficiently presented by the same tumor cell lines, except for one that expressed high level of immunoproteasome. It was only presented when the tumor cells were first IFN-γ treated, followed by infection with recombinant vaccinia virus encoding NY-ESO-1, which dramatically increased NY-ESO-1 expression. These data indicate that the presentation of NY-ESO-1<sub>88–96</sub> is immunoproteasome dependent. Furthermore, a survey was conducted on multiple samples collected from HLA-B18+ melanoma patients. Surprisingly, all the detectable responses to NY-ESO-1<sub>88–96</sub> from patients, including those who received NY-ESO-1 ISCOMATRIX™ vaccine were induced spontaneously. Taken together, these results imply that some epitopes can be inefficiently presented by tumor cells although the corresponding CD8<sup>+</sup>T cell responses are efficiently primed in vivo by DCs cross-presenting these epitopes. The potential implications for cancer vaccine strategies are further discussed

Integrated random processes exhibiting long tails, finite moments and 1/f spectra

A dynamical model based on a continuous addition of colored shot noises is presented. The resulting process is colored and non-Gaussian. A general expression for the characteristic function of the process is obtained, which, after a scaling assumption, takes on a form that is the basis of the results derived in the rest of the paper. One of these is an expansion for the cumulants, which are all finite, subject to mild conditions on the functions defining the process. This is in contrast with the Levy distribution -which can be obtained from our model in certain limits- which has no finite moments. The evaluation of the power spectrum and the form of the probability density function in the tails of the distribution shows that the model exhibits a 1/f spectrum and long tails in a natural way. A careful analysis of the characteristic function shows that it may be separated into a part representing a Levy processes together with another part representing the deviation of our model from the Levy process. This allows our process to be viewed as a generalization of the Levy process which has finite moments.Comment: Revtex (aps), 15 pages, no figures. Submitted to Phys. Rev.

Curve counting via stable pairs in the derived category

For a nonsingular projective 3-fold $X$, we define integer invariants virtually enumerating pairs $(C,D)$ where $C\subset X$ is an embedded curve and $D\subset C$ is a divisor. A virtual class is constructed on the associated moduli space by viewing a pair as an object in the derived category of $X$. The resulting invariants are conjecturally equivalent, after universal transformations, to both the Gromov-Witten and DT theories of $X$. For Calabi-Yau 3-folds, the latter equivalence should be viewed as a wall-crossing formula in the derived category. Several calculations of the new invariants are carried out. In the Fano case, the local contributions of nonsingular embedded curves are found. In the local toric Calabi-Yau case, a completely new form of the topological vertex is described. The virtual enumeration of pairs is closely related to the geometry underlying the BPS state counts of Gopakumar and Vafa. We prove that our integrality predictions for Gromov-Witten invariants agree with the BPS integrality. Conversely, the BPS geometry imposes strong conditions on the enumeration of pairs.Comment: Corrected typos and duality error in Proposition 4.6. 47 page

Ultrametricity and Memory in a Solvable Model of Self-Organized Criticality

Slowly driven dissipative systems may evolve to a critical state where long periods of apparent equilibrium are punctuated by intermittent avalanches of activity. We present a self-organized critical model of punctuated equilibrium behavior in the context of biological evolution, and solve it in the limit that the number of independent traits for each species diverges. We derive an exact equation of motion for the avalanche dynamics from the microscopic rules. In the continuum limit, avalanches propagate via a diffusion equation with a nonlocal, history-dependent potential representing memory. This nonlocal potential gives rise to a non-Gaussian (fat) tail for the subdiffusive spreading of activity. The probability for the activity to spread beyond a distance $r$ in time $s$ decays as $\sqrt{24\over\pi}s^{-3/2}x^{1/3} \exp{[-{3\over 4}x^{1/3}]}$ for $x={r^4\over s} \gg 1$. The potential represents a hierarchy of time scales that is dynamically generated by the ultrametric structure of avalanches, which can be quantified in terms of ``backward'' avalanches. In addition, a number of other correlation functions characterizing the punctuated equilibrium dynamics are determined exactly.Comment: 44 pages, Revtex, (12 ps-figures included