Identifying feasible operating regimes for early T-cell recognition: The speed, energy, accuracy trade-off in kinetic proofreading and adaptive sorting

In the immune system, T cells can quickly discriminate between foreign and self ligands with high accuracy. There is evidence that T-cells achieve this remarkable performance utilizing a network architecture based on a generalization of kinetic proofreading (KPR). KPR-based mechanisms actively consume energy to increase the specificity beyond what is possible in equilibrium.An important theoretical question that arises is to understand the trade-offs and fundamental limits on accuracy, speed, and dissipation (energy consumption) in KPR and its generalization. Here, we revisit this question through numerical simulations where we simultaneously measure the speed, accuracy, and energy consumption of the KPR and adaptive sorting networks for different parameter choices. Our simulations highlight the existence of a 'feasible operating regime' in the speed-energy-accuracy plane where T-cells can quickly differentiate between foreign and self ligands at reasonable energy expenditure. We give general arguments for why we expect this feasible operating regime to be a generic property of all KPR-based biochemical networks and discuss implications for our understanding of the T cell receptor circuit.Comment: 14 pages, 8 figure

Acoustic Communication for Medical Nanorobots

Communication among microscopic robots (nanorobots) can coordinate their activities for biomedical tasks. The feasibility of in vivo ultrasonic communication is evaluated for micron-size robots broadcasting into various types of tissues. Frequencies between 10MHz and 300MHz give the best tradeoff between efficient acoustic generation and attenuation for communication over distances of about 100 microns. Based on these results, we find power available from ambient oxygen and glucose in the bloodstream can readily support communication rates of about 10,000 bits/second between micron-sized robots. We discuss techniques, such as directional acoustic beams, that can increase this rate. The acoustic pressure fields enabling this communication are unlikely to damage nearby tissue, and short bursts at considerably higher power could be of therapeutic use.Comment: added discussion of communication channel capacity in section

Amorphous Placement and Retrieval of Sensory Data in Sparse Mobile Ad-Hoc Networks

Abstract—Personal communication devices are increasingly being equipped with sensors that are able to passively collect information from their surroundings – information that could be stored in fairly small local caches. We envision a system in which users of such devices use their collective sensing, storage, and communication resources to query the state of (possibly remote) neighborhoods. The goal of such a system is to achieve the highest query success ratio using the least communication overhead (power). We show that the use of Data Centric Storage (DCS), or directed placement, is a viable approach for achieving this goal, but only when the underlying network is well connected. Alternatively, we propose, amorphous placement, in which sensory samples are cached locally and informed exchanges of cached samples is used to diffuse the sensory data throughout the whole network. In handling queries, the local cache is searched first for potential answers. If unsuccessful, the query is forwarded to one or more direct neighbors for answers. This technique leverages node mobility and caching capabilities to avoid the multi-hop communication overhead of directed placement. Using a simplified mobility model, we provide analytical lower and upper bounds on the ability of amorphous placement to achieve uniform field coverage in one and two dimensions. We show that combining informed shuffling of cached samples upon an encounter between two nodes, with the querying of direct neighbors could lead to significant performance improvements. For instance, under realistic mobility models, our simulation experiments show that amorphous placement achieves 10% to 40% better query answering ratio at a 25% to 35% savings in consumed power over directed placement.National Science Foundation (CNS Cybertrust 0524477, CNS NeTS 0520166, CNS ITR 0205294, EIA RI 0202067

Thermal Baths as Quantum Resources: More Friends than Foes?

In this article we argue that thermal reservoirs (baths) are potentially useful resources in processes involving atoms interacting with quantized electromagnetic fields and their applications to quantum technologies. One may try to suppress the bath effects by means of dynamical control, but such control does not always yield the desired results. We wish instead to take advantage of bath effects, that do not obliterate "quantumness" in the system-bath compound. To this end, three possible approaches have been pursued by us: (i) Control of a quantum system faster than the correlation time of the bath to which it couples: Such control allows us to reveal quasi-reversible/coherent dynamical phenomena of quantum open systems, manifest by the quantum Zeno or anti-Zeno effects (QZE or AZE, respectively). Dynamical control methods based on the QZE are aimed not only at protecting the quantumness of the system, but also diagnosing the bath spectra or transferring quantum information via noisy media. By contrast, AZE-based control is useful for fast cooling of thermalized quantum systems. (ii) Engineering the coupling of quantum systems to selected bath modes: This approach, based on field -atom coupling control in cavities, waveguides and photonic band structures, allows to drastically enhance the strength and range of atom-atom coupling through the mediation of the selected bath modes. More dramatically, it allows us to achieve bath-induced entanglement that may appear paradoxical if one takes the conventional view that coupling to baths destroys quantumness. (iii) Engineering baths with appropriate non-flat spectra: This approach is a prerequisite for the construction of the simplest and most efficient quantum heat machines (engines and refrigerators). We may thus conclude that often thermal baths are "more friends than foes" in quantum technologies.Comment: 27 pages, 17 figure

Digital implementation of the cellular sensor-computers

Two different kinds of cellular sensor-processor architectures are used nowadays in various applications. The first is the traditional sensor-processor architecture, where the sensor and the processor arrays are mapped into each other. The second is the foveal architecture, in which a small active fovea is navigating in a large sensor array. This second architecture is introduced and compared here. Both of these architectures can be implemented with analog and digital processor arrays. The efficiency of the different implementation types, depending on the used CMOS technology, is analyzed. It turned out, that the finer the technology is, the better to use digital implementation rather than analog

Are there new models of computation? Reply to Wegner and Eberbach

Wegner and Eberbach[Weg04b] have argued that there are fundamental limitations to Turing Machines as a foundation of computability and that these can be overcome by so-called superTuring models such as interaction machines, the [pi]calculus and the $-calculus. In this paper we contest Weger and Eberbach claims