Casting Polymer Nets to Optimize Noisy Molecular Codes

Life relies on the efficient performance of molecular codes, which relate symbols and meanings via error-prone molecular recognition. We describe how optimizing a code to withstand the impact of molecular recognition noise may be approximated by the statistics of a two-dimensional network made of polymers. The noisy code is defined by partitioning the space of symbols into regions according to their meanings. The "polymers" are the boundaries between these regions and their statistics defines the cost and the quality of the noisy code. When the parameters that control the cost-quality balance are varied, the polymer network undergoes a first-order transition, where the number of encoded meanings rises discontinuously. Effects of population dynamics on the evolution of molecular codes are discussed.Comment: PNAS 200

Remarks on Bootstrap Percolation in Metric Networks

We examine bootstrap percolation in d-dimensional, directed metric graphs in the context of recent measurements of firing dynamics in 2D neuronal cultures. There are two regimes, depending on the graph size N. Large metric graphs are ignited by the occurrence of critical nuclei, which initially occupy an infinitesimal fraction, f_* -> 0, of the graph and then explode throughout a finite fraction. Smaller metric graphs are effectively random in the sense that their ignition requires the initial ignition of a finite, unlocalized fraction of the graph, f_* >0. The crossover between the two regimes is at a size N_* which scales exponentially with the connectivity range \lambda like_* \sim \exp\lambda^d. The neuronal cultures are finite metric graphs of size N \simeq 10^5-10^6, which, for the parameters of the experiment, is effectively random since N<< N_*. This explains the seeming contradiction in the observed finite f_* in these cultures. Finally, we discuss the dynamics of the firing front

Protein-DNA computation by stochastic assembly cascade

The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan DNA sequence through a cascade of random nucleation and disassembly events that is mechanistically similar to the dynamic instability of microtubules. This iterative cascade is a multistage kinetic proofreading process that amplifies minute differences, even a single base change. Our measurements suggest that this stochastic Turing-like machine can compute certain integral transforms.Comment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129313/ http://www.pnas.org/content/99/18/11589.abstrac

Molecular Model of the Contractile Ring

We present a model for the actin contractile ring of adherent animal cells. The model suggests that the actin concentration within the ring and consequently the power that the ring exerts both increase during contraction. We demonstrate the crucial role of actin polymerization and depolymerization throughout cytokinesis, and the dominance of viscous dissipation in the dynamics. The physical origin of two phases in cytokinesis dynamics ("biphasic cytokinesis") follows from a limitation on the actin density. The model is consistent with a wide range of measurements of the midzone of dividing animal cells.Comment: PACS numbers: 87.16.Ka, 87.16.Ac http://www.ncbi.nlm.nih.gov/pubmed/16197254 http://www.weizmann.ac.il/complex/tlusty/papers/PhysRevLett2005.pd

Thermodynamics and structure of self-assembled networks

We study a generic model of self-assembling chains which can branch and form networks with branching points (junctions) of arbitrary functionality. The physical realizations include physical gels, wormlike micells, dipolar fluids and microemulsions. The model maps the partition function of a solution of branched, self-assembling, mutually avoiding clusters onto that of a Heisenberg magnet in the mathematical limit of zero spin components. The model is solved in the mean field approximation. It is found that despite the absence of any specific interaction between the chains, the entropy of the junctions induces an effective attraction between the monomers, which in the case of three-fold junctions leads to a first order reentrant phase separation between a dilute phase consisting mainly of single chains, and a dense network, or two network phases. Independent of the phase separation, we predict the percolation (connectivity) transition at which an infinite network is formed that partially overlaps with the first-order transition. The percolation transition is a continuous, non thermodynamic transition that describes a change in the topology of the system. Our treatment which predicts both the thermodynamic phase equilibria as well as the spatial correlations in the system allows us to treat both the phase separation and the percolation threshold within the same framework. The density-density correlation correlation has a usual Ornstein-Zernicke form at low monomer densities. At higher densities, a peak emerges in the structure factor, signifying an onset of medium-range order in the system. Implications of the results for different physical systems are discussed.Comment: Submitted to Phys. Rev.

Phonons in a one-dimensional microfluidic crystal

The development of a general theoretical framework for describing the behaviour of a crystal driven far from equilibrium has proved difficult1. Microfluidic crystals, formed by the introduction of droplets of immiscible fluid into a liquid-filled channel, provide a convenient means to explore and develop models to describe non-equilibrium dynamics2, 3, 4, 5, 6, 7, 8, 9, 10, 11. Owing to the fact that these systems operate at low Reynolds number (Re), in which viscous dissipation of energy dominates inertial effects, vibrations are expected to be over-damped and contribute little to their dynamics12, 13, 14. Against such expectations, we report the emergence of collective normal vibrational modes (equivalent to acoustic 'phonons') in a one-dimensional microfluidic crystal of water-in-oil droplets at Reapprox10-4. These phonons propagate at an ultra-low sound velocity of approx100 mum s-1 and frequencies of a few hertz, exhibit unusual dispersion relations markedly different to those of harmonic crystals, and give rise to a variety of crystal instabilities that could have implications for the design of commercial microfluidic systems. First-principles theory shows that these phonons are an outcome of the symmetry-breaking flow field that induces long-range inter-droplet interactions, similar in nature to those observed in many other systems including dusty plasma crystals15, 16, vortices in superconductors17, 18, active membranes19 and nucleoprotein filaments20.Comment: https://www.weizmann.ac.il/complex/tlusty/papers/NaturePhys2006.pd

On the stability of high-speed milling with spindle speed variation

Spindle speed variation is a well-known technique to suppress regenerative machine tool vibrations, but it is usually considered to be effective only for low spindle speeds. In this paper, the effect of spindle speed variation is analyzed in the high-speed domain for spindle speeds corresponding to the first flip (period doubling) and to the first Hopf lobes. The optimal amplitudes and frequencies of the speed modulations are computed using the semidiscre- tization method. It is shown that period doubling chatter can effectively be suppressed by spindle speed variation, although, the technique is not effective for the quasiperiodic chatter above the Hopf lobe. The results are verified by cutting tests. Some special cases are also discussed where the practical behavior of the system differs from the predicted one in some ways. For these cases, it is pointed out that the concept of stability is understood on the scale of the principal period of the system—that is, the speed modulation period for variable spindle speed machining and the tooth passing period for constant spindle speed machining

Model and parameter dependence of heavy quark energy loss in a hot and dense medium

Within the framework of the Langevin equation, we study the energy loss of heavy quark due to quasi-elastic multiple scatterings in a quark-gluon plasma created by relativistic heavy-ion collisions. We investigate how the initial configuration of the quark-gluon plasma as well as its properties affect the final state spectra and elliptic flow of D meson and non-photonic electron. We find that both the geometric anisotropy of the initial quark-gluon plasma and the flow profiles of the hydrodynamic medium play important roles in the heavy quark energy loss process and the development of elliptic flow. The relative contribution from charm and bottom quarks is found to affect the transverse momentum dependence of the quenching and flow patterns of heavy flavor decay electron; such influence depends on the interaction strength between heavy quark and the medium.Comment: 16 pages, 7 figure

Electromagnetic Calorimeter for HADES

We propose to build the Electromagnetic calorimeter for the HADES di-lepton spectrometer. It will enable to measure the data on neutral meson production from nucleus-nucleus collisions, which are essential for interpretation of dilepton data, but are unknown in the energy range of planned experiments (2-10 GeV per nucleon). The calorimeter will improve the electron-hadron separation, and will be used for detection of photons from strange resonances in elementary and HI reactions. Detailed description of the detector layout, the support structure, the electronic readout and its performance studied via Monte Carlo simulations and series of dedicated test experiments is presented. The device will cover the total area of about 8 m^2 at polar angles between 12 and 45 degrees with almost full azimuthal coverage. The photon and electron energy resolution achieved in test experiments amounts to 5-6%/sqrt(E[GeV]) which is sufficient for the eta meson reconstruction with S/B ratio of 0.4% in Ni+Ni collisions at 8 AGeV. A purity of the identified leptons after the hadron rejection, resulting from simulations based on the test measurements, is better than 80% at momenta above 500 MeV/c, where time-of-flight cannot be used.Comment: 40 pages, 38 figures version2 - the time schedule added, information about PMTs in Sec.III update

Domain regime in two-dimensional disordered vortex matter

A detailed numerical study of the real space configuration of vortices in disordered superconductors using 2D London-Langevin model is presented. The magnetic field $B$ is varied between 0 and $B_{c2}$ for various pinning strengths $\Delta$. For weak pinning, an inhomogeneous disordered vortex matter is observed, in which the topologically ordered vortex lattice survives in large domains. The majority of the dislocations in this state are confined to the grain boundaries/domain walls. Such quasi-ordered configurations are observed in the intermediate fields, and we refer it as the domain regime (DR). The DR is distinct from the low-field and the high-fields amorphous regimes which are characterized by a homogeneous distribution of defects over the entire system. Analysis of the real space configuration suggests domain wall roughening as a possible mechanism for the crossover from the DR to the high-field amorphous regime. The DR also shows a sharp crossover to the high temperature vortex liquid phase. The domain size distribution and the roughness exponent of the lattice in the DR are also calculated. The results are compared with some of the recent Bitter decoration experiments.Comment: 9 pages, 9 figure