The thermodynamics of computational copying in biochemical systems

Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that, as in computation, a canonical biochemical readout network generates correlations; extracting no work from these correlations sets a lower bound on dissipation. For general input, the biochemical network cannot reach this bound, even with arbitrarily slow reactions or weak thermodynamic driving. It faces an accuracy-dissipation trade-off that is qualitatively distinct from and worse than implied by the bound, and more complex steady-state copy processes cannot perform better. Nonetheless, the cost remains close to the thermodynamic bound unless accuracy is extremely high. Additionally, we show that biomolecular reactions could be used in thermodynamically optimal devices under exogenous manipulation of chemical fuels, suggesting an experimental system for testing computational thermodynamics.Comment: Accepted versio

Implementation of polarization diversity pulse-pair technique using airborne W-band radar

This work describes the implementation of polarization diversity on the National Research Council Canada W-band Doppler radar and presents the first-ever airborne Doppler measurements derived via polarization diversity pulse-pair processing. The polarization diversity pulse-pair measurements are interleaved with standard pulse-pair measurements with staggered pulse repetition frequency, this allows a better understanding of the strengths and drawbacks of polarization diversity, a methodology that has been recently proposed for wind-focused Doppler radar space missions. Polarization diversity has the clear advantage of making possible Doppler observations of very fast decorrelating media (as expected when deploying Doppler radars on fast-moving satellites) and of widening the Nyquist interval, thus enabling the observation of very high Doppler velocities (up to more than 100 m s−1 in the present work). Crosstalk between the two polarizations, mainly caused by depolarization at backscattering, deteriorated the quality of the observations by introducing ghost echoes in the power signals and by increasing the noise level in the Doppler measurements. In the different cases analyzed during the field campaigns, the regions affected by crosstalk were generally associated with highly depolarized surface returns and depolarization of backscatter from hydrometeors located at short ranges from the aircraft. The variance of the Doppler velocity estimates can be well predicted from theory and were also estimated directly from the observed correlation between the H-polarized and V-polarized successive pulses. The study represents a key milestone towards the implementation of polarization diversity in Doppler space-borne radars

Multiplexing Biochemical Signals

In this paper we show that living cells can multiplex biochemical signals, i.e. transmit multiple signals through the same signaling pathway simultaneously, and yet respond to them very specifically. We demonstrate how two binary input signals can be encoded in the concentration of a common signaling protein, which is then decoded such that each of the two output signals provides reliable information about one corresponding input. Under biologically relevant conditions the network can reach the maximum amount of information that can be transmitted, which is 2 bits.Comment: 4 pages, 4 figure

Sampling rare switching events in biochemical networks

Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because switching events are rapid, yet infrequent. We present a simulation technique that makes it possible to predict the rate and mechanism of flipping of biochemical switches. The method uses a series of interfaces in phase space between the two stable steady states of the switch to generate transition trajectories in a ratchet-like manner. We demonstrate its use by calculating the spontaneous flipping rate of a symmetric model of a genetic switch consisting of two mutually repressing genes. The rate constant can be obtained orders of magnitude more efficiently than using brute-force simulations. For this model switch, we show that the switching mechanism, and consequently the switching rate, depends crucially on whether the binding of one regulatory protein to the DNA excludes the binding of the other one. Our technique could also be used to study rare events and non-equilibrium processes in soft condensed matter systems.Comment: 9 pages, 6 figures, last page contains supplementary informatio

Implementation of polarization diversity pulse-pair technique using airborne W-band radar

This work describes the implementation of polarization diversity on the National Research Council Canada W-band Doppler radar and presents the first-ever airborne Doppler measurements derived via polarization diversity pulse-pair processing. The polarization diversity pulse-pair measurements are interleaved with standard pulse-pair measurements with staggered pulse repetition frequency, this allows a better understanding of the strengths and drawbacks of polarization diversity, a methodology that has been recently proposed for wind-focused Doppler radar space missions. Polarization diversity has the clear advantage of making possible Doppler observations of very fast decorrelating media (as expected when deploying Doppler radars on fast-moving satellites) and of widening the Nyquist interval, thus enabling the observation of very high Doppler velocities (up to more than 100m -1 in the present work). Crosstalk between the two polarizations, mainly caused by depolarization at backscattering, deteriorated the quality of the observations by introducing ghost echoes in the power signals and by increasing the noise level in the Doppler measurements. In the different cases analyzed during the field campaigns, the regions affected by crosstalk were generally associated with highly depolarized surface returns and depolarization of backscatter from hydrometeors located at short ranges from the aircraft. The variance of the Doppler velocity estimates can be well predicted from theory and were also estimated directly from the observed correlation between the H-polarized and inline-formula V-polarized successive pulses. The study represents a key milestone towards the implementation of polarization diversity in Doppler space-borne radars

Finding the center reliably: robust patterns of developmental gene expression

We investigate a mechanism for the robust identification of the center of a developing biological system. We assume the existence of two morphogen gradients, an activator emanating from the anterior, and a co-repressor from the posterior. The co-repressor inhibits the action of the activator in switching on target genes. We apply this system to Drosophila embryos, where we predict the existence of a hitherto undetected posterior co-repressor. Using mathematical modelling, we show that a symmetric activator-co-repressor model can quantitatively explain the precise mid-embryo expression boundary of the hunchback gene, and the scaling of this pattern with embryo size.Comment: 4 pages, 3 figure

A Steepest Feasible Direction Method for Linear Programming. Derivation and Embedding In the Simplex Method

A feasible direction method for linear programming has been proposed. The method is embedded in the framework of the simplex method, even though it works with non-edge feasible directions. The direction used is the steepest in the space of all variables or an approximation thereof, and it is found by solving a strictly convex quadratic program in the space of the nonbasic variables. Further, this program guarantees the feasibility of the direction even in the case of degeneracy. To remain within the simplex framework, the direction is represented by an auxiliary, or external, nonbasic column, which is a nonnegative linear combination of original nonbasic columns. We have made an experimental evaluation of the suggested method on both nondegenerate and highly degenerate problem instances. The overall results are very promising for continued research along this line, especially concerning various computational strategies that can be applied when the method is implemented. (original abstract

Triple frequency radar retrieval of microphysical properties of snow

An algorithm based on triple-frequency (X, Ka, W) radar measurements that retrieves the size, water content and degree of riming of ice clouds is presented. This study exploits the potential of multi-frequency radar measurements to provide information on bulk snow density that should underpin better estimates of the snow characteristic size and content within the radar volume. The algorithm is based on Bayes' rule with riming parameterised by the “fill-in” model. The radar reflectivities are simulated with a range of scattering models corresponding to realistic snowflake shapes. The algorithm is tested on multi-frequency radar data collected during the ESA-funded Radar Snow Experiment For Future Precipitation Mission. During this campaign, in situ microphysical probes were mounted on the same aeroplane as the radars. This nearly perfectly co-located dataset of the remote and in situ measurements gives an opportunity to derive a combined multi-instrument estimate of snow microphysical properties that is used for a rigorous validation of the radar retrieval. Results suggest that the triple-frequency retrieval performs well in estimating ice water content (IWC) and mean mass-weighted diameters obtaining root-mean-square errors of 0.13 and 0.15, respectively, for log 10IWC and log 10Dm. The retrieval of the degree of riming is more challenging, and only the algorithm that uses Doppler information obtains results that are highly correlated with the in situ data.</p