Tiling solutions for optimal biological sensing

Biological systems, from cells to organisms, must respond to the ever changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically stochastic, many body and often self-organized nature of the processes that control their sensing and response and limited resources. Despite a wide range of scales and functions that can be observed in the living world, some common principles that govern the behavior of biological systems emerge. Here I review two examples of very different biological problems: information transmission in gene regulatory networks and diversity of adaptive immune receptor repertoires that protect us from pathogens. I discuss the trade-offs that physical laws impose on these systems and show that the optimal designs of both immune repertoires and gene regulatory networks display similar discrete tiling structures. These solutions rely on locally non-overlapping placements of the responding elements (genes and receptors) that, overall, cover space nearly uniformly.Comment: 11 page

Pairing Fluctuation AC Conductivity of Disordered Thin Films

We study temperature $T$ and frequency $\omega$ dependence of the in-plane fluctuation conductivity of a disordered superconducting film above the critical temperature. Our calculation is based on the nonlinear sigma model within the Keldysh technique. The fluctuation contributions of different physical origin are found and analyzed in a wide frequency range. In the low-frequency range, $\omega\ll T$, we reproduce the known leading terms and find additional subleading ones in the Aslamazov-Larkin and the Maki-Thompson contributions to the ac conductivity. We also calculate the density of states ac correction. In the dc case these contributions logarithmically depend on the Ginzburg-Landau rate and are considerably smaller that the leading ones. However, in the ac case an external finite-frequency electromagnetic field strongly suppresses the known Alsamazov-Larkin and Maki-Thompson ac contributions, while the corresponding new terms and the density of states contribution are weakly suppressed and therefore become relevant at finite frequencies.Comment: 14 page

Electron production by solar Ly-{\alpha} line radiation in the ionospheric D-region

The hydrogen Ly-{\alpha} line has a dominant influence in photo-ionization processes in the unperturbed terrestrial ionospheric D region. In this paper, we present a procedure of calculating the rate of photo-ionization induced by Ly-{\alpha} photons based on relaxation of electron density after intensive perturbations like those caused by solar X flares. This theory is applied to the ends of relaxation periods following three cases of solar X flares from May 5, 2010, February 18, 2011 and March 24, 2011. The necessary data on low ionospheric plasma parameters were collected by the very low frequency (VLF) radio-wave technics. The electron concentration is calculated from the amplitude and phase of the VLF signal emitted by the DHO transmitter in Germany and recorded by a receiver located in Serbia.Comment: 9 pages, 6 figure, 2 table

Combining Slater-type orbitals and effective core potentials

We present a general methodology to evaluate matrix elements of the effective core potentials (ECPs) within one-electron basis set of Slater-type orbitals (STOs). The scheme is based on translation of individual STO distributions in the framework of Barnett-Coulson method. We discuss different types of integrals which naturally appear and reduce them to few basic quantities which can be calculated recursively or purely numerically. Additionally, we consider evaluation of the STOs matrix elements involving the core polarisation potentials (CPP) and effective spin-orbit potentials. Construction of the STOs basis sets designed specifically for use with ECPs is discussed and differences in comparison with all-electron basis sets are briefly summarised. We verify the validity of the present approach by calculating excitation energies, static dipole polarisabilities and valence orbital energies for the alkaline earth metals (Ca, Sr, Ba). Finally, we evaluate interaction energies, permanent dipole moments and ionisation energies for barium and strontium hydrides, and compare them with the best available experimental and theoretical data.Comment: submitted to Phys. Rev.