Fluctuation Theorem with Information Exchange: Role of Correlations in Stochastic Thermodynamics

We establish the fluctuation theorem in the presence of information exchange between a nonequilibrium system and other degrees of freedom such as an observer and a feedback controller, where the amount of information exchange is added to the entropy production. The resulting generalized second law sets the fundamental limit of energy dissipation and energy cost during the information exchange. Our results apply not only to feedback-controlled processes but also to a much broader class of information exchanges, and provides a unified framework of nonequilibrium thermodynamics of measurement and feedback control.Comment: To appear in PR

Energy-Efficient Algorithms

We initiate the systematic study of the energy complexity of algorithms (in addition to time and space complexity) based on Landauer's Principle in physics, which gives a lower bound on the amount of energy a system must dissipate if it destroys information. We propose energy-aware variations of three standard models of computation: circuit RAM, word RAM, and transdichotomous RAM. On top of these models, we build familiar high-level primitives such as control logic, memory allocation, and garbage collection with zero energy complexity and only constant-factor overheads in space and time complexity, enabling simple expression of energy-efficient algorithms. We analyze several classic algorithms in our models and develop low-energy variations: comparison sort, insertion sort, counting sort, breadth-first search, Bellman-Ford, Floyd-Warshall, matrix all-pairs shortest paths, AVL trees, binary heaps, and dynamic arrays. We explore the time/space/energy trade-off and develop several general techniques for analyzing algorithms and reducing their energy complexity. These results lay a theoretical foundation for a new field of semi-reversible computing and provide a new framework for the investigation of algorithms.Comment: 40 pages, 8 pdf figures, full version of work published in ITCS 201

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 explana- tions for the alignment of the two arrows will be briefly discussed.Comment: 31 pages, no figures, publication versio

Opening up the Quantum Three-Box Problem with Undetectable Measurements

One of the most striking features of quantum mechanics is the profound effect exerted by measurements alone. Sophisticated quantum control is now available in several experimental systems, exposing discrepancies between quantum and classical mechanics whenever measurement induces disturbance of the interrogated system. In practice, such discrepancies may frequently be explained as the back-action required by quantum mechanics adding quantum noise to a classical signal. Here we implement the 'three-box' quantum game of Aharonov and Vaidman in which quantum measurements add no detectable noise to a classical signal, by utilising state-of-the-art control and measurement of the nitrogen vacancy centre in diamond. Quantum and classical mechanics then make contradictory predictions for the same experimental procedure, however classical observers cannot invoke measurement-induced disturbance to explain this discrepancy. We quantify the residual disturbance of our measurements and obtain data that rule out any classical model by > 7.8 standard deviations, allowing us for the first time to exclude the property of macroscopic state-definiteness from our system. Our experiment is then equivalent to a Kochen-Spekker test of quantum non-contextuality that successfully addresses the measurement detectability loophole

Energy and eventhood: the infrastructural set piece

‘Energy and Eventhood’ considers the relationship between infrastructure and the cinematic set piece. It proposes a working definition of the set piece as a distinctly (and perhaps excessively) effortful passage or sequence, and reflects on the tendency for narrative films to incorporate infrastructural sites and structures—such as bridges, dams and pipelines—into such set pieces. A number of writers on infrastructure, as both a cultural phenomenon and a representational object, have noted the aesthetic challenge of rendering it as visible and locatable; this article examines how that difficulty becomes manifest in the infrastructural set piece. It takes as its case studies Unstoppable (2010) and Night Moves (2013), two films noted for their distinctive rhythmic expressiveness, and each one deploying the convention of the set piece in ways which exemplify and reflect on the resistance of infrastructure to narrative containment

Brief for Respondents, Grutter v. Bollinger, 539 US 306 (2003) (No. 02-241).

QUESTIONS PRESENTED 1. Whether this Court should reaffirm its decision in Regents of University of California v. Bakke, 438 U.S. 265 (1978) and hold that the educational benefits that flow from a diverse student body to an institution of higher education, its students, and the public it serves, are sufficiently compelling to permit the school to consider race and/or ethnicity as one of many factors in making admissions decisions through a properly devised admissions program. 2. Whether the Court of Appeals correctly held that the University of Michigan Law School\u27s admissions program is properly devised

A novel class of microRNA-recognition elements that function only within open reading frames.

MicroRNAs (miRNAs) are well known to target 3' untranslated regions (3' UTRs) in mRNAs, thereby silencing gene expression at the post-transcriptional level. Multiple reports have also indicated the ability of miRNAs to target protein-coding sequences (CDS); however, miRNAs have been generally believed to function through similar mechanisms regardless of the locations of their sites of action. Here, we report a class of miRNA-recognition elements (MREs) that function exclusively in CDS regions. Through functional and mechanistic characterization of these 'unusual' MREs, we demonstrate that CDS-targeted miRNAs require extensive base-pairing at the 3' side rather than the 5' seed; cause gene silencing in an Argonaute-dependent but GW182-independent manner; and repress translation by inducing transient ribosome stalling instead of mRNA destabilization. These findings reveal distinct mechanisms and functional consequences of miRNAs that target CDS versus the 3' UTR and suggest that CDS-targeted miRNAs may use a translational quality-control-related mechanism to regulate translation in mammalian cells

Consequences of temperature fluctuations in observables measured in high energy collisions

We review the consequences of intrinsic, nonstatistical temperature fluctuations as seen in observables measured in high energy collisions. We do this from the point of view of nonextensive statistics and Tsallis distributions. Particular attention is paid to multiplicity fluctuations as a first consequence of temperature fluctuations, to the equivalence of temperature and volume fluctuations, to the generalized thermodynamic fluctuations relations allowing us to compare fluctuations observed in different parts of phase space, and to the problem of the relation between Tsallis entropy and Tsallis distributions. We also discuss the possible influence of conservation laws on these distributions and provide some examples of how one can get them without considering temperature fluctuations.Comment: Revised version of the invited contribution to The European Physical Journal A (Hadrons and Nuclei) topical issue about 'Relativistic Hydro- and Thermodynamics in Nuclear Physics' guest eds. Tamas S. Biro, Gergely G. Barnafoldi and Peter Va

A Candidate Approach Implicates the Secreted Salmonella Effector Protein SpvB in P-Body Disassembly

P-bodies are dynamic aggregates of RNA and proteins involved in several post-transcriptional regulation processes. P-bodies have been shown to play important roles in regulating viral infection, whereas their interplay with bacterial pathogens, specifically intracellular bacteria that extensively manipulate host cell pathways, remains unknown. Here, we report that Salmonella infection induces P-body disassembly in a cell type-specific manner, and independently of previously characterized pathways such as inhibition of host cell RNA synthesis or microRNA-mediated gene silencing. We show that the Salmonella-induced P-body disassembly depends on the activation of the SPI-2 encoded type 3 secretion system, and that the secreted effector protein SpvB plays a major role in this process. P-body disruption is also induced by the related pathogen, Shigella flexneri, arguing that this might be a new mechanism by which intracellular bacterial pathogens subvert host cell function

Comparative Genomic and Transcriptomic Characterization of the Toxigenic Marine Dinoflagellate Alexandrium ostenfeldii

Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regulation, such as spliced leader (SL) trans-splicing and mRNA transposition mechanisms. Alexandrium ostenfeldii is known to produce macrocyclic imine toxins, described as spirolides. We characterized the genome of A. ostenfeldii using a combination of transcriptomic data and random genomic clones for comparison with other dinoflagellates, particularly Alexandrium species. Examination of SL sequences revealed similar features as in other dinoflagellates, including Alexandrium species. SL sequences in decay indicate frequent retro-transposition of mRNA species. This probably contributes to overall genome complexity by generating additional gene copies. Sequencing of several thousand fosmid and bacterial artificial chromosome (BAC) ends yielded a wealth of simple repeats and tandemly repeated longer sequence stretches which we estimated to comprise more than half of the whole genome. Surprisingly, the repeats comprise a very limited set of 79–97 bp sequences; in part the genome is thus a relatively uniform sequence space interrupted by coding sequences. Our genomic sequence survey (GSS) represents the largest genomic data set of a dinoflagellate to date. Alexandrium ostenfeldii is a typical dinoflagellate with respect to its transcriptome and mRNA transposition but demonstrates Alexandrium-like stop codon usage. The large portion of repetitive sequences and the organization within the genome is in agreement with several other studies on dinoflagellates using different approaches. It remains to be determined whether this unusual composition is directly correlated to the exceptionally genome organization of dinoflagellates with a low amount of histones and histone-like proteins