Search

We propose a physically-realisable biochemical device that is coupled to a biochemical reservoir of mutual information, fuel molecules and a chemical bath. Mutual information allows work to be done on the bath even when the fuel molecules appear to be in equilibrium; alternatively, mutual information can be created by driving from the fuel or the bath. The system exhibits diverse behaviour, including a regime in which the information, despite increasing during the reaction, enhances the extracted work. We further demonstrate that a modified device can function without the need for external manipulation, eliminating the need for a complex and potentially costly control.

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.

To measure chemical concentrations, cells need to extract information from stochastic receptor signals via signaling networks which are also inherently stochastic. Here, we study how the accuracy of sensing depends on the correlations between these extrinsic and intrinsic sources of noise. We find that the sensing precision of signaling networks that are not driven out of equilibrium is fundamentally limited by the fluctuation-dissipation theorem, which generates a tradeoff between the removal of extrinsic and intrinsic noise. As a result, the sensing precision of equilibrium systems is limited by the number of receptors; the downstream network can never improve sensing. To lift the tradeoff, energy dissipation is essential. This allows the receptor to transduce the signal as a catalyst and enables time integration of the receptor state. To beat the sensing limit of equilibrium systems, a canonical nonequilibrium signaling network based on the push-pull motif needs to dissipate at least 1k_{B}T per receptor.

We report computer simulations of homogeneous gas-liquid nucleation in a model for strongly polar fluids. We find that, in the early stages of the nucleation process, chainlike clusters are formed. Beyond a certain size, these collapse to form compact spherical clusters. However, the interface of the collapsed nuclei differs markedly from the planar interface. Classical nucleation theory underestimates both the size of the critical nucleus and the height of the nucleation barrier.

Living cells often need to extract information from biochemical signals that are noisy. We study how accurately cells can measure chemical concentrations with signaling networks that are linear. For stationary signals of long duration, they can reach, but not beat, the Berg-Purcell limit, which relies on uniformly averaging in time the fluctuations in the input signal. For short times or nonstationary signals, however, they can beat the Berg-Purcell limit, by non-uniformly time-averaging the input. We derive the optimal weighting function for time averaging and use it to provide the fundamental limit of measuring chemical concentrations with linear signaling networks., Comment: To appear in Physical Review Letters, 7 pages, 4 figures

We study the kinetics of crystal nucleation of an undercooled Lennard-Jones liquid using various path-sampling methods. We obtain the rate constant and elucidate the pathways for crystal nucleation. Analysis of the path ensemble reveals that crystal nucleation occurs along many different pathways, in which critical solid nuclei can be small, compact, and face centered cubic, but also large, less ordered, and more body centered cubic. The reaction coordinate thus includes, besides the cluster size, also the quality of the crystal structure.

We present a technique, called Green's function reaction dynamics (GFRD), for particle-based simulations of reaction-diffusion systems. GFRD uses a maximum time step such that only single particles or pairs of particles have to be considered. For these particles, the Smoluchowski equations are solved analytically using Green's functions, which are used to set up an event-driven algorithm. We apply the technique to a model of gene expression. Under biologically relevant conditions, GFRD is up to 5 orders of magnitude faster than conventional particle-based schemes. © 2005 The American Physical Society.

We study genetic switches formed from pairs of mutually repressing operons. The switch stability is characterised by a well defined lifetime which grows sub-exponentially with the number of copies of the most-expressed transcription factor, in the regime accessible by our numerical simulations. The stability can be markedly enhanced by a suitable choice of overlap between the upstream regulatory domains. Our results suggest that robustness against biochemical noise can provide a selection pressure that drives operons, that regulate each other, together in the course of evolution., 4 pages, 5 figures, RevTeX4

We have observed a radially localized electron wave packet in a direct pump-probe experiment with 6-ps laser pulses. Use is made of the fact that both excitation and ionization take place predominantly close to the atomic core. A wave packet is created by coherently exciting Rydberg states of rubidium atoms around $n=41$ with a pump pulse, and detected through ionization with a delayed probe pulse. The wave packet is observed to return to the core twice before the spreading becomes too large.