Entangled Wavefunctions from Classical Oscillator Amplitudes

In the first days of quantum mechanics Dirac pointed out an analogy between the time-dependent coefficients of an expansion of the Schr\"odinger equation and the classical position and momentum variables solving Hamilton's equations. Here it is shown that the analogy can be made an equivalence in that, in principle, systems of classical oscillators can be constructed whose position and momenta variables form time-dependent amplitudes which are identical to the complex quantum amplitudes of the coupled wavefunction of an N-level quantum system with real coupling matrix elements. Hence classical motion can reproduce quantum coherence.Comment: extended versio

Full counting statistics of strongly non-Ohmic transport through single molecules

We study analytically the full counting statistics of charge transport through single molecules, strongly coupled to a weakly damped vibrational mode. The specifics of transport in this regime - a hierarchical sequence of avalanches of transferred charges, interrupted by "quiet" periods - make the counting statistics strongly non-Gaussian. We support our findings for the counting statistics as well as for the frequency-dependent noise power by numerical simulations, finding excellent agreement.Comment: 4+ pages, 2 figures; minor changes, version published in Phys. Rev. Let

Clustering in gravitating N-body systems

We study gravitational clustering of mass points in three dimensions with random initial positions and periodic boundary conditions (no expansion) by numerical simulations. Correlation properties are well defined in the system and a sort of thermodynamic limit can be defined for the transient regime of cluste ring. Structure formation proceeds along two paths: (i) fluid-like evolution of density perturbations at large scales and (ii) shift of the granular (non fluid) properties from small to large scales. The latter mechanism finally dominates at all scales and it is responsible for the self-similar characteristics of the clustering.Comment: 7 pages, 3 figures. Accepted for publication in Europhys. Let

Probability distribution function of dipolar field in two-dimensional spin ensemble

We theoretically determine the probability distribution function of the net field of the random planar structure of dipoles which represent polarized particles. At small surface concentrations c of the point dipoles this distribution is expressed in terms of special functions. At the surface concentrations of the dipoles as high as 0.6 the dipolar field obey the Gaussian law. To obtain the distribution function within transitional region c<0.6, we propose the method based on the cumulant expansion. We calculate the parameters of the distributions for some specific configurations of the dipoles. The distribution functions of the ordered ensembles of the dipoles at the low and moderate surface concentrations have asymmetric shape with respect to distribution medians. The distribution functions allow to calculate various physical parameters of two-dimensional interacting nanoparticle ensembles.Comment: 9 pages, 3 figure

Microfield distributions in strongly coupled two-component plasmas

The electric microfield distribution at charged particles is studied for two-component electron-ion plasmas using molecular dynamics simulation and theoretical models. The particles are treated within classical statistical mechanics using an electron-ion Coulomb potential regularized at distances less than the de Broglie length to take into account the quantum-diffraction effects. The potential-of-mean-force (PMF) approximation is deduced from a canonical ensemble formulation. The resulting probability density of the electric microfield satisfies exactly the second-moment sum rule without the use of adjustable parameters. The correlation functions between the charged radiator and the plasma ions and electrons are calculated using molecular dynamics simulations and the hypernetted-chain approximation for a two-component plasma. It is shown that the agreement between the theoretical models for the microfield distributions and the simulations is quite good in general.Comment: 18 figures. Submitted to Phys. Rev.

On the nature of gravitational forces

In this paper I show how the statistics of the gravitational field is changed when the system is characterized by a non-uniform distribution of particles. I show how the distribution functions W(dF/dt) giving the joint probability that a test particle is subject to a force F and an associated rate of change of F given by dF/dt, are modified by inhomogeneity. Then I calculate the first moment of dF/dt to study the effects of inhomogenity on dynamical friction. Finally I test, by N-Body simulations, that the theoretical W(F) and dF/dt describes correctly the experimental data and I find that the stochastic force distribution obtained for the evolved system is in good agreement with theory. Moreover, I find that in an inhomogeneous background the friction force is actually enhanced relative to the homogeneous case

Renormalized cluster expansion of the microfield distribution in a strongly coupled two-component plasmas

The electric microfield distribution (MFD) at an impurity ion is studied for two-component (TCP) electron-ion plasmas using molecular dynamics simulation and theoretical models. The particles are treated within classical statistical mechanics using an electron-ion Coulomb potential regularized at distances less than the de Broglie length to take into account quantum-diffraction effects. Corrections to the potential-of-mean-force exponential (PMFEX) approximation recently proposed for MFD in a strongly coupled TCP [Phys. Rev. E 72, 036403 (2005)] are obtained and discussed. This has been done by a generalization of the standard Baranger-Mozer and renormalized cluster expansion techniques originally developed for the one-component plasmas to the TCPs. The results obtained for a neutral point are compared with those from molecular dynamics simulations. It is shown that the corrections do not help to improve the PMFEX approximation for a TCP with low ionic charge Z. But starting with Z > 5 the PMFEX model is substantially improved and the agreement with numerical simulations is excellent. We have also found that with increasing coupling the PMFEX approximation becomes invalid to predict the MFD at a neutral point while its corrected version agrees satisfactory with the simulations.Comment: 17 pages, 10 figures, submitted to Physical Review

Statistics of the gravitational force in various dimensions of space: from Gaussian to Levy laws

We discuss the distribution of the gravitational force created by a Poissonian distribution of field sources (stars, galaxies,...) in different dimensions of space d. In d=3, it is given by a Levy law called the Holtsmark distribution. It presents an algebraic tail for large fluctuations due to the contribution of the nearest neighbor. In d=2, it is given by a marginal Gaussian distribution intermediate between Gaussian and Levy laws. In d=1, it is exactly given by the Bernouilli distribution (for any particle number N) which becomes Gaussian for N>>1. Therefore, the dimension d=2 is critical regarding the statistics of the gravitational force. We generalize these results for inhomogeneous systems with arbitrary power-law density profile and arbitrary power-law force in a d-dimensional universe

BAGEL2: mining for bacteriocins in genomic data

Mining bacterial genomes for bacteriocins is a challenging task due to the substantial structure and sequence diversity, and generally small sizes, of these antimicrobial peptides. Major progress in the research of antimicrobial peptides and the ever-increasing quantities of genomic data, varying from (un)finished genomes to meta-genomic data, led us to develop the significantly improved genome mining software BAGEL2, as a follow-up of our previous BAGEL software. BAGEL2 identifies putative bacteriocins on the basis of conserved domains, physical properties and the presence of biosynthesis, transport and immunity genes in their genomic context. The software supports parameter-free, class-specific mining and has high-throughput capabilities. Besides building an expert validated bacteriocin database, we describe the development of novel Hidden Markov Models (HMMs) and the interpretation of combinations of HMMs via simple decision rules for prediction of bacteriocin (sub-)classes. Furthermore, the genetic context is automatically annotated based on (combinations of) PFAM domains and databases of known context genes. The scoring system was fine-tuned using expert knowledge on data derived from screening all bacterial genomes currently available at the NCBI. BAGEL2 is freely accessible at http://bagel2.molgenrug.nl

Bioenergy as climate change mitigation option within a 2 °C target—uncertainties and temporal challenges of bioenergy systems

Bioenergy is given an important role in reaching national and international climate change targets. However, uncertainties relating to emission reductions and the timeframe for these reductions are increasingly recognised as challenges whether bioenergy can deliver the required reductions. This paper discusses and highlights the challenges and the importance of the real greenhouse gas (GHG) reduction potential of bioenergy systems and its relevance for a global 450 ppm CO2e stabilisation target in terms of uncertainties and temporal aspects. The authors aim to raise awareness and emphasise the need for dynamic and consequential approaches for the evaluation of climate change impacts of bioenergy systems to capture the complexity and challenges of their real emission reduction potential within a 2 °C target. This review does not present new research results. This paper shows the variety of challenges and complexity of the problem of achieving real GHG emission reductions from bioenergy systems. By reflecting on current evaluation methods of emissions and impacts from bioenergy systems, this review points out that a rethinking and going beyond static approaches is required, considering each bioenergy systems according to its own characteristics, context and feedbacks. With the development of knowledge and continuously changing systems, policies should be designed in a way that they provide a balance between flexibility to adapt to new information and planning security for investors. These will then allow considering if a bioenergy system will deliver the required emission saving in the appropriate timeframe or not