Linear models of activation cascades: analytical solutions and coarse-graining of delayed signal transduction

Cellular signal transduction usually involves activation cascades, the sequential activation of a series of proteins following the reception of an input signal. Here we study the classic model of weakly activated cascades and obtain analytical solutions for a variety of inputs. We show that in the special but important case of optimal-gain cascades (i.e., when the deactivation rates are identical) the downstream output of the cascade can be represented exactly as a lumped nonlinear module containing an incomplete gamma function with real parameters that depend on the rates and length of the cascade, as well as parameters of the input signal. The expressions obtained can be applied to the non-identical case when the deactivation rates are random to capture the variability in the cascade outputs. We also show that cascades can be rearranged so that blocks with similar rates can be lumped and represented through our nonlinear modules. Our results can be used both to represent cascades in computational models of differential equations and to fit data efficiently, by reducing the number of equations and parameters involved. In particular, the length of the cascade appears as a real-valued parameter and can thus be fitted in the same manner as Hill coefficients. Finally, we show how the obtained nonlinear modules can be used instead of delay differential equations to model delays in signal transduction.Comment: 18 pages, 7 figure

Stiff Stability of the Hydrogen atom in dissipative Fokker electrodynamics

We introduce an ad-hoc electrodynamics with advanced and retarded Lienard-Wiechert interactions plus the dissipative Lorentz-Dirac self-interaction force. We study the covariant dynamical system of the electromagnetic two-body problem, i.e., the hydrogen atom. We perform the linear stability analysis of circular orbits for oscillations perpendicular to the orbital plane. In particular we study the normal modes of the linearized dynamics that have an arbitrarily large imaginary eigenvalue. These large eigenvalues are fast frequencies that introduce a fast (stiff) timescale into the dynamics. As an application, we study the phenomenon of resonant dissipation, i.e., a motion where both particles recoil together in a drifting circular orbit (a bound state), while the atom dissipates center-of-mass energy only. This balancing of the stiff dynamics is established by the existence of a quartic resonant constant that locks the dynamics to the neighborhood of the recoiling circular orbit. The resonance condition quantizes the angular momenta in reasonable agreement with the Bohr atom. The principal result is that the emission lines of quantum electrodynamics (QED) agree with the prediction of our resonance condition within one percent average deviation.Comment: 1 figure, Notice that Eq. (34) of the Phys. Rev. E paper has a typo; it is missing the square Brackets of eq. (33), find here the correct e

Fluctuation theorem for constrained equilibrium systems

We discuss the fluctuation properties of equilibrium chaotic systems with constraints such as iso-kinetic and Nos\'e-Hoover thermostats. Although the dynamics of these systems does not typically preserve phase-space volumes, the average phase-space contraction rate vanishes, so that the stationary states are smooth. Nevertheless finite-time averages of the phase-space contraction rate have non-trivial fluctuations which we show satisfy a simple version of the Gallavotti-Cohen fluctuation theorem, complementary to the usual fluctuation theorem for non-equilibrium stationary states, and appropriate to constrained equilibrium states. Moreover we show these fluctuations are distributed according to a Gaussian curve for long-enough times. Three different systems are considered here, namely (i) a fluid composed of particles interacting with Lennard-Jones potentials; (ii) a harmonic oscillator with Nos\'e-Hoover thermostatting; (iii) a simple hyperbolic two-dimensional map.Comment: To appear in Phys. Rev.

Cosmological particle production and the precision of the WKB approximation

Particle production by slow-changing gravitational fields is usually described using quantum field theory in curved spacetime. Calculations require a definition of the vacuum state, which can be given using the adiabatic (WKB) approximation. I investigate the best attainable precision of the resulting approximate definition of the particle number. The standard WKB ansatz yields a divergent asymptotic series in the adiabatic parameter. I derive a novel formula for the optimal number of terms in that series and demonstrate that the error of the optimally truncated WKB series is exponentially small. This precision is still insufficient to describe particle production from vacuum, which is typically also exponentially small. An adequately precise approximation can be found by improving the WKB ansatz through perturbation theory. I show quantitatively that the fundamentally unavoidable imprecision in the definition of particle number in a time-dependent background is equal to the particle production expected to occur during that epoch. The results are illustrated by analytic and numerical examples.Comment: 14 pages, RevTeX, 5 figures; minor changes, a clarification in Sec. II

Polarization Selection Rules and Superconducting Gap Anisotropy in Bi2Sr2CaCu2O8Bi_2Sr_2CaCu_2O_8

We discuss polarization selection rules for angle-resolved photoemission spectroscopy in Bi2212. Using these we show that the ``hump'' in the superconducting gap observed in the $X$ quadrant in our earlier work is not on the main $CuO_2$ band, but rather on an umklapp band arising from the structural superlattice. The intrinsic gap is most likely quite small over a range of $\pm 10^\circ$ about the diagonal directions.Comment: 3 pages, revtex, 3 uuencoded postscript figure

Brownian motion with dry friction: Fokker-Planck approach

We solve a Langevin equation, first studied by de Gennes, in which there is a solid-solid or dry friction force acting on a Brownian particle in addition to the viscous friction usually considered in the study of Brownian motion. We obtain both the time-dependent propagator of this equation and the velocity correlation function by solving the associated time-dependent Fokker-Planck equation. Exact results are found for the case where only dry friction acts on the particle. For the case where both dry and viscous friction forces are present, series representations of the propagator and correlation function are obtained in terms of parabolic cylinder functions. Similar series representations are also obtained for the case where an external constant force is added to the Langevin equation.Comment: 18 pages, 13 figures (in color

Dynamical derivation of Bode's law

In a planetary or satellite system, idealized as n small bodies in initially coplanar, concentric orbits around a large central body, obeying Newtonian point-particle mechanics, resonant perturbations will cause dynamical evolution of the orbital radii except under highly specific mutual relationships, here derived analytically apparently for the first time. In particular, the most stable situation is achieved (in this idealized model) only when each planetary orbit is roughly twice as far from the Sun as the preceding one, as observed empirically already by Titius (1766) and Bode (1778) and used in both the discoveries of Uranus (1781) and the Asteroid Belt (1801). ETC.Comment: 27 page

Computers from plants we never made. Speculations

We discuss possible designs and prototypes of computing systems that could be based on morphological development of roots, interaction of roots, and analog electrical computation with plants, and plant-derived electronic components. In morphological plant processors data are represented by initial configuration of roots and configurations of sources of attractants and repellents; results of computation are represented by topology of the roots' network. Computation is implemented by the roots following gradients of attractants and repellents, as well as interacting with each other. Problems solvable by plant roots, in principle, include shortest-path, minimum spanning tree, Voronoi diagram, $\alpha$-shapes, convex subdivision of concave polygons. Electrical properties of plants can be modified by loading the plants with functional nanoparticles or coating parts of plants of conductive polymers. Thus, we are in position to make living variable resistors, capacitors, operational amplifiers, multipliers, potentiometers and fixed-function generators. The electrically modified plants can implement summation, integration with respect to time, inversion, multiplication, exponentiation, logarithm, division. Mathematical and engineering problems to be solved can be represented in plant root networks of resistive or reaction elements. Developments in plant-based computing architectures will trigger emergence of a unique community of biologists, electronic engineering and computer scientists working together to produce living electronic devices which future green computers will be made of.Comment: The chapter will be published in "Inspired by Nature. Computing inspired by physics, chemistry and biology. Essays presented to Julian Miller on the occasion of his 60th birthday", Editors: Susan Stepney and Andrew Adamatzky (Springer, 2017

Direct observation of particle-hole mixing in the superconducting state by angle-resolved photoemission

Particle-hole (p-h) mixing is a fundamental consequence of the existence of a pair condensate. We present direct experimental evidence for p-h mixing in the angle-resolved photoemission (ARPES) spectra in the superconducting state of Bi_2Sr_2CaCu_2O_{8+\delta}. In addition to its pedagogical importance, this establishes unambiguously that the gap observed in ARPES is associated with superconductivity.Comment: 3 pages, revtex, 4 postscript figure

Optimal Fleet Composition via Dynamic Programming and Golden Section Search

In this paper, we consider an optimization problem arising in vehicle fleet management. The problem is to construct a heterogeneous vehicle fleet in such a way that cost is minimized subject to a constraint on the overall fleet size. The cost function incorporates fixed and variable costs associated with the fleet, as well as hiring costs that are incurred when vehicle requirements exceed fleet capacity. We first consider the simple case when there is only one type of vehicle. We show that in this case the cost function is convex, and thus the problem can be solved efficiently using the well-known golden section method. We then devise an algorithm, based on dynamic programming and the golden section method, for solving the general problem in which there are multiple vehicle types. We conclude the paper with some simulation results