Does a computer have an arrow of time?

In [Sch05a], it is argued that Boltzmann's intuition, that the psychological arrow of time is necessarily aligned with the thermodynamic arrow, is correct. Schulman gives an explicit physical mechanism for this connection, based on the brain being representable as a computer, together with certain thermodynamic properties of computational processes. [Haw94] presents similar, if briefer, arguments. The purpose of this paper is to critically examine the support for the link between thermodynamics and an arrow of time for computers. The principal arguments put forward by Schulman and Hawking will be shown to fail. It will be shown that any computational process that can take place in an entropy increasing universe, can equally take place in an entropy decreasing universe. This conclusion does not automatically imply a psychological arrow can run counter to the thermodynamic arrow. Some alternative possible explanations for the alignment of the two arrows will be briefly discussed

Decoherence Strength of Multiple Non-Markovian Environments

It is known that one can characterize the decoherence strength of a Markovian environment by the product of its temperature and induced damping, and order the decoherence strength of multiple environments by this quantity. We show that for non-Markovian environments in the weak coupling regime there also exists a natural (albeit partial) ordering of environment-induced irreversibility within a perturbative treatment. This measure can be applied to both low-temperature and non-equilibrium environments.Comment: 6 pages, 1 figure, v3 included figure, appendix, and clarification of result

Exact analytical solutions to the master equation of quantum Brownian motion for a general environment

We revisit the model of a quantum Brownian oscillator linearly coupled to an environment of quantum oscillators at finite temperature. By introducing a compact and particularly well-suited formulation, we give a rather quick and direct derivation of the master equation and its solutions for general spectral functions and arbitrary temperatures. The flexibility of our approach allows for an immediate generalization to cases with an external force and with an arbitrary number of Brownian oscillators. More importantly, we point out an important mathematical subtlety concerning boundary-value problems for integro-differential equations which led to incorrect master equation coefficients and impacts on the description of nonlocal dissipation effects in all earlier derivations. Furthermore, we provide explicit, exact analytical results for the master equation coefficients and its solutions in a wide variety of cases, including ohmic, sub-ohmic and supra-ohmic environments with a finite cut-off.Comment: 37 pages (26 + appendices), 14 figures; this paper is an evolution of arXiv:0705.2766v1, but contains far more general and significant results; v2 minor changes, double column, improved Appendix

Rheology of a confined granular material

We study the rheology of a granular material slowly driven in a confined geometry. The motion is characterized by a steady sliding with a resistance force increasing with the driving velocity and the surrounding relative humidity. For lower driving velocities a transition to stick-slip motion occurs, exhibiting a blocking enhancement whith decreasing velocity. We propose a model to explain this behavior pointing out the leading role of friction properties between the grains and the container's boundary.Comment: 9 pages, 3 .eps figures, submitted to PR

Fluctuations of an evaporating black hole from back reaction of its Hawking radiation: Questioning a premise in earlier work

This paper delineates the first steps in a systematic quantitative study of the spacetime fluctuations induced by quantum fields in an evaporating black hole. We explain how the stochastic gravity formalism can be a useful tool for that purpose within a low-energy effective field theory approach to quantum gravity. As an explicit example we apply it to the study of the spherically-symmetric sector of metric perturbations around an evaporating black hole background geometry. For macroscopic black holes we find that those fluctuations grow and eventually become important when considering sufficiently long periods of time (of the order of the evaporation time), but well before the Planckian regime is reached. In addition, the assumption of a simple correlation between the fluctuations of the energy flux crossing the horizon and far from it, which was made in earlier work on spherically-symmetric induced fluctuations, is carefully analyzed and found to be invalid. Our analysis suggests the existence of an infinite amplitude for the fluctuations of the horizon as a three-dimensional hypersurface. We emphasize the need for understanding and designing operational ways of probing quantum metric fluctuations near the horizon and extracting physically meaningful information.Comment: 10 pages, REVTeX; minor changes, a few references added and a brief discussion of their relevance included. To appear in the proceedings of the 10th Peyresq meeting. Dedicated to Rafael Sorkin on the occasion of his 60th birthda

Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

A Taxonomy of Causality-Based Biological Properties

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the implication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the characterization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form calculus. We illustrate an application of this framework to a portion of a real metabolic pathway

Towards elucidating carnosic acid biosynthesis in Lamiaceae: Functional characterization of the three first steps of the pathway in Salvia fruticosa and Rosmarinus officinalis

Carnosic acid (CA) is a phenolic diterpene with anti-tumour, anti-diabetic, antibacterial and neuroprotective properties that is produced by a number of species from several genera of the Lamiaceae family, including Salvia fruticosa (Cretan sage) and Rosmarinus officinalis (Rosemary). To elucidate CA biosynthesis, glandular trichome transcriptome data of S. fruticosa were mined for terpene synthase genes. Two putative diterpene synthase genes, namely SfCPSand SfKSL, showing similarities to copalyl diphosphate synthase and kaurene synthase-like genes, respectively, were isolated and functionally characterized. Recombinant expression in Escherichia coli followed by in vitro enzyme activity assays confirmed that SfCPS is a copalyl diphosphate synthase. Coupling of SfCPS with SfKSL, both in vitro and in yeast, resulted in the synthesis miltiradiene, as confirmed by 1D and 2D NMR analyses (1H, 13C, DEPT, COSY H-H, HMQC and HMBC). Coupled transient in vivo assays of SfCPS and SfKSL in Nicotiana benthamiana further confirmed production of miltiradiene in planta. To elucidate the subsequent biosynthetic step, RNA-Seq data of S. fruticosa and R. officinalis were searched for cytochrome P450 (CYP) encoding genes potentially involved in the synthesis of the first phenolic compound in the CA pathway, ferruginol. Three candidate genes were selected, SfFS, RoFS1 and RoFS2. Using yeast and N. benthamiana expression systems, all three where confirmed to be coding for ferruginol synthases, thus revealing the enzymatic activities responsible for the first three steps leading to CA in two Lamiaceae genera

The effect of online hemodiafiltration on infections: Results from the CONvective TRAnsport STudy

Background: Hemodialysis (HD) patients have a high risk of infections. The uremic milieu has a negative impact on several immune responses. Online hemodiafiltration (HDF) may reduce the risk of infections by ameliorating the uremic milieu through enhanced clearance of middle molecules. Since there are few data on infectious outcomes in HDF, we compared the effects of HDF with low-flux HD on the incidence and type of infections. Patients and Methods: We used data of the 714 HD patients (age 64 ±14, 62% men, 25% Diabetes Mellitus, 7% catheters) participating in the CONvective TRAnsport STudy (CONTRAST), a randomized controlled trial evaluating the effect of HDF as compared to low-flux HD. The events were adjudicated by an independent event committee. The risk of infectious events was compared with Cox regression for repeated events and Cox proportional hazard models. The distributions of types of infection were compared between the groups. Results: Thirty one percent of the patients suffered from one or more infections leading to hospitalization during the study (median follow-up 1.96 years). The risk for infections during the entire follow-up did not differ significantly between treatment arms (HDF 198 and HD 169 infections in 800 and 798 person-years respectively, hazard ratio HDF vs. HD 1.09 (0.88-1.34), P = 0.42. No difference was found in the occurrence of the first infectious event (either fatal, nonfatal or type specific). Of all infections, respiratory infections (25% in HDF, 28% in HD) were most common, followed by skin/musculoskeletal infections (21% in HDF, 13% in HD). Conclusions: HDF as compared to HD did not result in a reduced risk of infections, larger studies are needed to confirm our findings. Trial Registration: ClinicalTrials.gov NCT00205556

Magnetization dynamics with a spin-transfer torque

The magnetization reversal and dynamics of a spin valve pillar, whose lateral size is 64$\times$64 nm$^2$, are studied by using micromagnetic simulation in the presence of spin transfer torque. Spin torques display both characteristics of magnetic damping (or anti-damping) and of an effective magnetic field. For a steady-state current, both M-I and M-H hysteresis loops show unique features, including multiple jumps, unusual plateaus and precessional states. These states originate from the competition between the energy dissipation due to Gilbert damping and the energy accumulation due to the spin torque supplied by the spin current. The magnetic energy oscillates as a function of time even for a steady-state current. For a pulsed current, the minimum width and amplitude of the spin torque for achieving current-driven magnetization reversal are quantitatively determined. The spin torque also shows very interesting thermal activation that is fundamentally different from an ordinary damping effect.Comment: 15 figure