13,090 research outputs found
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 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
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