Comment on "Chain Length Scaling of Protein Folding Time", PRL 77, 5433 (1996)

In a recent Letter, Gutin, Abkevich, and Shakhnovich (GAS) reported on a series of dynamical Monte Carlo simulations on lattice models of proteins. Based on these highly simplified models, they found that four different potential energies lead to four different folding time scales tau_f, where tau_f scales with chain length as N^lambda (see, also, Refs. [2-4]), with lambda varying from 2.7 to 6.0. However, due to the lack of microscopic models of protein folding dynamics, the interpretation and origin of the data have remained somewhat speculative. It is the purpose of this Comment to point out that the application of a simple "mesoscopic" model (cond-mat/9512019, PRL 77, 2324, 1996) of protein folding provides a full account of the data presented in their paper. Moreover, we find a major qualitative disagreement with the argumentative interpretation of GAS. Including, the origin of the dynamics, and size of the critical folding nucleus.Comment: 1 page Revtex, 1 fig. upon request. Submitted to PR

Scarcity may promote cooperation in populations of simple agents

In the study of the evolution of cooperation, resource limitations are usually assumed just to provide a finite population size. Recently, however, it has been pointed out that resource limitation may also generate dynamical payoffs able to modify the original structure of the games. Here we study analytically a phase transition from a homogeneous population of defectors when resources are abundant to the survival of unconditional cooperators when resources reduce below a threshold. To this end, we introduce a model of simple agents, with no memory or ability of recognition, interacting in well-mixed populations. The result might shed light on the role played by resource constraints on the origin of multicellularity.Comment: 5 pages, 2 figure

Identifying structures in the continuum: Application to 16^{16}Be

The population and decay of two-nucleon resonances offer exciting new opportunities to explore dripline phenomena. The understanding of these systems requires a solid description of the three-body (core+N+N) continuum. The identification of a state with resonant character from the background of non-resonant continuum states in the same energy range poses a theoretical challenge. It is the purpose of this work to establish a robust theoretical framework to identify and characterize three-body resonances in a discrete basis. A resonance operator is proposed, which describes the sensitivity to changes in the potential. Resonances are then identified from the lowest eigenstates of the resonance operator. The operator is diagonalized in a basis of Hamiltonian pseudostates, built within the hyperspherical harmonics formalism using the analytical THO basis. The energy and width of the resonance are determined from its time dependence. The method is applied to 16Be in a 14Be+n+n model. An effective core+n potential, fitted to the available information on the subsystem 15Be, is employed. The 0+ ground state resonance of 16Be presents a strong dineutron configuration, which favors the picture of a correlated two-neutron emission. Fitting the three body interaction to the experimental two-neutron separation energy |S2n|=1.35(10) MeV, the computed width is Gamma(0+)=0.16 MeV. From the same Hamiltonian, a 2+ resonance is also predicted with E_r(2+)=2.42 MeV and Gamma(2+)=0.40 MeV. The dineutron configuration and the computed 0+ width are consistent with previous R-matrix calculations for the true three-body continuum. The extracted values of the resonance energy and width converge with the size of the pseudostate basis and are robust under changes in the basis parameters. This supports the reliability of the method in describing the properties of unbound core+N+N systems in a discrete basis.Comment: 11 pages, 14 figures. Accepted as PR

A Criterion That Determines Fast Folding of Proteins: A Model Study

We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model, the typical time scale for reaching the unique native conformation is shown to scale as $\tau_f\sim F(M)\exp(\sigma/\sigma_0)$, where $\sigma=1-T_f/T_\theta$, $M$ is the number of residues, and $F(M)$ scales algebraically with $M$. We argue that $T_f$ scales linearly with the inverse of entropy of low energy non-native states, whereas $T_\theta$ is almost independent of it. As $\sigma\rightarrow 0$, non-productive intermediates decrease, and the initial rapid collapse of the protein leads to structures resembling the native state. Based solely on {\it accessible} information, $\sigma$ can be used to predict sequences that fold rapidly.Comment: 10 pages, latex, figures upon reques

Positronium lifetime in polymers

A model describing the relationship between the ortho--positronium lifetime and the volume of a void, located in a synthetic zeolite, is analyzed. Our idea, which allows us to take into account the effects of temperature, comprises the introduction of a non--hermitian term in the Hamiltonian, which accounts for the annihilation of the ortho--positronium. The predictions of the present model are also confronted against an already known experimental result.Comment: Accepted in Journal of Chemical Physic

Analytical models for well-mixed populations of cooperators and defectors under limiting resources

In the study of the evolution of cooperation, resource limitations are usually assumed just to provide a finite population size. Recently, however, agent-based models have pointed out that resource limitation may modify the original structure of the interactions and allow for the survival of unconditional cooperators in well-mixed populations. Here, we present analytical simplified versions of two types of agent-based models recently published: one in which the limiting resource constrains the ability of reproduction of individuals but not their survival, and a second one where the limiting resource is necessary for both reproduction and survival. One finds that the analytical models display, with a few differences, the same qualitative behavior of the more complex agent-based models. In addition, the analytical models allow us to expand the study and identify the dimensionless parameters governing the final fate of the system, such as coexistence of cooperators and defectors, or dominance of defectors or of cooperators. We provide a detailed analysis of the occurring phase transitions as these parameters are varied.Comment: 7 pages, 8 figure

Wear of a chute in a rice sorting machine

In a rice sorting machine, rice grains drop onto and slide down an anodised aluminium chute. The purpose of the chute is to separate the grains and provide a controlled distribution. At the bottom of the chute the grains are examined optically and contaminants or defective grains are removed from the stream by jets of air. The machine has the ability to sort low quality rice which contains a large element of contaminants such as husk. The husk is extremely abrasive and this, along with other factors, can lead to a reduction in the life of the chute by wear of the surface. In this work a failure analysis process was undertaken to establish the nature and causes of the chute surface wear and the mechanisms of material removal. Wear occurs initially at the location where the grains first strike the chute and at subsequent regions down the chute where bounce occurs. An experimental and analytical examination of the rice motion on impacting the chute was also carried out along with some friction testing of potential replacement chute materials. The evidence gathered during the failure analysis along with the experimental analysis was used to propose possible material/design improvements

Determining B(E1)B(E1) distributions of weakly bound nuclei from breakup cross sections using Continuum Discretized Coupled Channels calculations. Application to 11^{11}Be

A novel method to extract the $B(E1)$ strength of a weakly bound nucleus from experimental Coulomb dissociation data is proposed. The method makes use of continuum discretized coupled channels (CDCC) calculations, in which both nuclear and Coulomb forces are taken into account to all orders. This is a crucial advantage with respect to the standard procedure based on the Equivalent Photon Method (EPM) which does not properly take into account nuclear distortion, higher order coupling effects, or Coulomb-nuclear interference terms. The procedure is applied to the $^{11}$Be nucleus using two sets of available experimental data at different energies, for which seemingly incompatible $B(E1)$ have been reported using the EPM. We show that the present procedure gives consistent $B(E1)$ strengths, thus solving the aforementioned long-standing discrepancy between the two measurements.Comment: Submitted for publicatio

Influence of oxygen pressure on the fs laserinduced oxidation of molybdenum thin films

We present a study of femtosecond (1028 nm, 230 fs, 54.7 MHz) laser processing on molybdenum (Mo) thin films. Irradiations were done under ambient air as well as pure oxygen (O2) at various gauge pressures (4, 8, 12 and 16 psi). Our results indicate that the high heating rates associated with laser processing allow the production of different molybdenum oxides. Raman spectroscopy and scanning electron microscopy are used to characterize the molybdenum oxidation for the different irradiation and oxygen pressures parameters chosen showing a high correlation between well-defined oxidation zones and the oxygen pressure surrounding the samples during the irradiation of the Mo thin films