Specific protein-protein binding in many-component mixtures of proteins

Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein, specific binding in many component mixtures is studied. It is found to be a demanding function in the sense that it demands that the binding sites of the proteins be encoded by long sequences of bits, and the requirement for specific binding then strongly constrains these sequences. This is quantified by the capacity of proteins of a given size (sequence length), which is the maximum number of specific-binding interactions possible in a mixture. This calculation of the maximum number possible is in the same spirit as the work of Shannon and others on the maximum rate of communication through noisy channels.Comment: 13 pages, 3 figures (changes for v2 mainly notational - to be more in line with notation in information theory literature

Thermodynamic time asymmetry in nonequilibrium fluctuations

We here present the complete analysis of experiments on driven Brownian motion and electric noise in a $RC$ circuit, showing that thermodynamic entropy production can be related to the breaking of time-reversal symmetry in the statistical description of these nonequilibrium systems. The symmetry breaking can be expressed in terms of dynamical entropies per unit time, one for the forward process and the other for the time-reversed process. These entropies per unit time characterize dynamical randomness, i.e., temporal disorder, in time series of the nonequilibrium fluctuations. Their difference gives the well-known thermodynamic entropy production, which thus finds its origin in the time asymmetry of dynamical randomness, alias temporal disorder, in systems driven out of equilibrium.Comment: to be published in : Journal of Statistical Mechanics: theory and experimen

Non-additivity of quantum capacity for multiparty communication channels

We investigate multiparty communication scenarios where information is sent from several sender to several receivers. We establish a relation between the quantum capacity of multiparty communication channels and their distillability properties which enables us to show that the quantum capacity of such channels is not additive.Comment: 4 pages, 1 figur

Entropy and Entanglement in Quantum Ground States

We consider the relationship between correlations and entanglement in gapped quantum systems, with application to matrix product state representations. We prove that there exist gapped one-dimensional local Hamiltonians such that the entropy is exponentially large in the correlation length, and we present strong evidence supporting a conjecture that there exist such systems with arbitrarily large entropy. However, we then show that, under an assumption on the density of states which is believed to be satisfied by many physical systems such as the fractional quantum Hall effect, that an efficient matrix product state representation of the ground state exists in any dimension. Finally, we comment on the implications for numerical simulation.Comment: 7 pages, no figure

Improving Detectors Using Entangling Quantum Copiers

We present a detection scheme which using imperfect detectors, and imperfect quantum copying machines (which entangle the copies), allows one to extract more information from an incoming signal, than with the imperfect detectors alone.Comment: 4 pages, 2 figures, REVTeX, to be published in Phys. Rev.

Managing weather and climate risks to agriculture in North America, Central America and the Caribbean

AbstractIn recent decades, numerous weather- and climate-related natural disasters have impacted North America, Central America, and the Caribbean, repeatedly demonstrating how vulnerable local agriculture is to extreme episodic events. Given this recent history, and expectations that the frequency and intensity of some episodic events will increase with climate change, it is becoming increasingly important for farmers to proactively manage weather and climate risks to agriculture to protect their livelihoods. Some farmers in this region already apply various strategies to help reduce weather and climate risks and uncertainties, including farming in multiple locations, diversifying crops and varieties, seeking alternative sources of income, and purchasing crop insurance. Such efforts often help farmers maintain a more stable income while also protecting and preserving the productivity of the land. Other farmers, however, have failed to implement basic risk management strategies despite the clear benefits. Reasons for these failures can be attributed to inadequate farmer education and training, a lack of tools to help facilitate the practical application of risk management concepts, and poor communications between the agrometeorological and farming communities. The agrometeorological community can help overcome these obstacles by building upon existing efforts that have successfully educated farmers about weather and climate risks to agriculture and have equipped farmers with the data, tools, and applications necessary to manage these risks. Farmer input is critical to preparing effective educational and training materials and developing user-friendly risk management tools. The agrometeorological community should solicit input from farmers regularly to ensure that farmers are obtaining the information necessary to effectively manage weather and climate risks to agriculture

Information capacity of genetic regulatory elements

Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform non-trivial computations that integrate several inputs and affect multiple genes. At the same time, the activities of the regulated genes would fluctuate even if the inputs were held fixed, as a consequence of the intrinsic noise in the system, and such noise must fundamentally limit the reliability of any genetic computation. Here we use information theory to formalize the notion of information transmission in simple genetic regulatory elements in the presence of physically realistic noise sources. The dependence of this "channel capacity" on noise parameters, cooperativity and cost of making signaling molecules is explored systematically. We find that, at least in principle, capacities higher than one bit should be achievable and that consequently genetic regulation is not limited the use of binary, or "on-off", components.Comment: 17 pages, 9 figure

cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models

The increasing availability of sequencing data of cancer samples is fueling the development of algorithmic strategies to investigate tumor heterogeneity and infer reliable models of cancer evolution. We here build up on previous works on cancer progression inference from genomic alteration data, to deliver two distinct Cytoscape-based applications, which allow to produce, visualize and manipulate cancer evolution models, also by interacting with public genomic and proteomics databases. In particular, we here introduce cyTRON, a stand-alone Cytoscape app, and cyTRON/JS, a web application which employs the functionalities of Cytoscape/JS. cyTRON was developed in Java; the code is available at https://github.com/BIMIB-DISCo/cyTRON and on the Cytoscape App Store http://apps.cytoscape.org/apps/cytron. cyTRON/JS was developed in JavaScript and R; the source code of the tool is available at https://github.com/BIMIB-DISCo/cyTRON-js and the tool is accessible from https://bimib.disco.unimib.it/cytronjs/welcome