Prediction and Power in Molecular Sensors: Uncertainty and Dissipation When Conditionally Markovian Channels Are Driven by Semi-Markov Environments

Sensors often serve at least two purposes: predicting their input and minimizing dissipated heat. However, determining whether or not a particular sensor is evolved or designed to be accurate and efficient is difficult. This arises partly from the functional constraints being at cross purposes and partly since quantifying the predictive performance of even in silico sensors can require prohibitively long simulations. To circumvent these difficulties, we develop expressions for the predictive accuracy and thermodynamic costs of the broad class of conditionally Markovian sensors subject to unifilar hidden semi-Markov (memoryful) environmental inputs. Predictive metrics include the instantaneous memory and the mutual information between present sensor state and input future, while dissipative metrics include power consumption and the nonpredictive information rate. Success in deriving these formulae relies heavily on identifying the environment's causal states, the input's minimal sufficient statistics for prediction. Using these formulae, we study the simplest nontrivial biological sensor model---that of a Hill molecule, characterized by the number of ligands that bind simultaneously, the sensor's cooperativity. When energetic rewards are proportional to total predictable information, the closest cooperativity that optimizes the total energy budget generally depends on the environment's past hysteretically. In this way, the sensor gains robustness to environmental fluctuations. Given the simplicity of the Hill molecule, such hysteresis will likely be found in more complex predictive sensors as well. That is, adaptations that only locally optimize biochemical parameters for prediction and dissipation can lead to sensors that "remember" the past environment.Comment: 21 pages, 4 figures, http://csc.ucdavis.edu/~cmg/compmech/pubs/piness.ht

Prediction and Dissipation in Nonequilibrium Molecular Sensors: Conditionally Markovian Channels Driven by Memoryful Environments.

Biological sensors must often predict their input while operating under metabolic constraints. However, determining whether or not a particular sensor is evolved or designed to be accurate and efficient is challenging. This arises partly from the functional constraints being at cross purposes and partly since quantifying the prediction performance of even in silico sensors can require prohibitively long simulations, especially when highly complex environments drive sensors out of equilibrium. To circumvent these difficulties, we develop new expressions for the prediction accuracy and thermodynamic costs of the broad class of conditionally Markovian sensors subject to complex, correlated (unifilar hidden semi-Markov) environmental inputs in nonequilibrium steady state. Predictive metrics include the instantaneous memory and the total predictable information (the mutual information between present sensor state and input future), while dissipation metrics include power extracted from the environment and the nonpredictive information rate. Success in deriving these formulae relies on identifying the environment's causal states, the input's minimal sufficient statistics for prediction. Using these formulae, we study large random channels and the simplest nontrivial biological sensor model-that of a Hill molecule, characterized by the number of ligands that bind simultaneously-the sensor's cooperativity. We find that the seemingly impoverished Hill molecule can capture an order of magnitude more predictable information than large random channels

Improved Carrier Blocking Properties of Interface in Cryogenic Particle Detectors

Sensitivity of cryogenic particle detectors suffers from various loss and leakage mechanisms which influence carrier transport in the bulk and interface layers of the detectors. Suppressing- and wherever possible, eliminating- such loss mechanisms is imperative to lowering the noise floor of detectors to enable detection of characteristically weak energy signatures of exotic particle interactions. This work investigates one such loss mechanism– tunneling driven carrier leakage through the interface stack in particle detectors– and focuses on remodeling the stack composition and associated fabrication processes to mitigate such leakage. Measures to improve carrier blocking properties in the interface are explored with an aim to lower the steady state leakage and thereby improve detector sensitivity. This study aims at identifying and implementing measures to combat carrier tunneling through the interface. As part of such efforts, novel distributions of 40nm interface-thickness budget of SiOv2 and poly-crystalline Silicon have been tested for their capabilities of suppressing tunneling mechanisms. This comes as a modification to the previously proposed 20nm+20nm configuration of SiO2+pc-Si which, while being a significant improvement over the traditionally used amorphous-Si interface, has still been shown to be inadequate in blocking carriers. Interface processing modifications aimed at suppressing trap-mediated tunneling mechanisms by way of annealing the devices following SiO2 deposition have been explored. Rapid thermal processing at 600 degrees C has been found to decrease the leakage by over an order of magnitude at 22K, which while being promising, still leaves room for improvement. CO2 laser annealing has been identified as an option for selectively annealing only the SiO2 film at high temperatures (~1500 degrees C) thereby leaving the substrate purity uncompromised. Laser annealing has been performed at different power levels and scan speeds to identify the highest usable temperature that does not result in pinhole defects in the film. Room temperature and cryogenic characterization has been performed on these devices to evaluate their carrier blocking properties. At 20K, laser annealed devices have been found to exhibit leakage three orders of magnitude lower than as deposited samples and two orders lower than rapid thermal processed devices

Improved Carrier Blocking Properties of Interface in Cryogenic Particle Detectors

Sensitivity of cryogenic particle detectors suffers from various loss and leakage mechanisms which influence carrier transport in the bulk and interface layers of the detectors. Suppressing- and wherever possible, eliminating- such loss mechanisms is imperative to lowering the noise floor of detectors to enable detection of characteristically weak energy signatures of exotic particle interactions. This work investigates one such loss mechanism– tunneling driven carrier leakage through the interface stack in particle detectors– and focuses on remodeling the stack composition and associated fabrication processes to mitigate such leakage. Measures to improve carrier blocking properties in the interface are explored with an aim to lower the steady state leakage and thereby improve detector sensitivity. This study aims at identifying and implementing measures to combat carrier tunneling through the interface. As part of such efforts, novel distributions of 40nm interface-thickness budget of SiOv2 and poly-crystalline Silicon have been tested for their capabilities of suppressing tunneling mechanisms. This comes as a modification to the previously proposed 20nm+20nm configuration of SiO2+pc-Si which, while being a significant improvement over the traditionally used amorphous-Si interface, has still been shown to be inadequate in blocking carriers. Interface processing modifications aimed at suppressing trap-mediated tunneling mechanisms by way of annealing the devices following SiO2 deposition have been explored. Rapid thermal processing at 600 degrees C has been found to decrease the leakage by over an order of magnitude at 22K, which while being promising, still leaves room for improvement. CO2 laser annealing has been identified as an option for selectively annealing only the SiO2 film at high temperatures (~1500 degrees C) thereby leaving the substrate purity uncompromised. Laser annealing has been performed at different power levels and scan speeds to identify the highest usable temperature that does not result in pinhole defects in the film. Room temperature and cryogenic characterization has been performed on these devices to evaluate their carrier blocking properties. At 20K, laser annealed devices have been found to exhibit leakage three orders of magnitude lower than as deposited samples and two orders lower than rapid thermal processed devices