Search results for "Ratchet"
showing 10 items of 17 documents
EVOLUTIONARY DYNAMICS OF FITNESS RECOVERY FROM THE DEBILITATING EFFECTS OF MULLER'S RATCHET.
1998
The great adaptability shown by RNA viruses is a consequence of their high mutation rates. The evolution of fitness in a severely debilitated, clonal population of the nonsegmented ribovirus vesicular stomatitis virus (VSV) has been compared under five different demographic regimes, ranging from severe serial bottleneck passages (one virion) to large population passages (105 virions or more) under similar environmental conditions (cell culture type and temperature). No matter how small the bottleneck, the fitness of the evolved populations was always higher than the fitness of the starting population; this result is clearly different from that previously reported for viruses with higher fit…
Diffusion Acceleration in Randomly Switching Sawtooth Potential
2005
We investigate an overdamped Brownian motion in symmetric sawtooth periodic potential switched by Markovian dichotomous noise between two configurations. The two configurations differ each other by a translation of half of period. The calculation of the effective diffusion coefficient is reduced to the mean first‐passage time problem, and we obtain the exact expression valid for arbitrary mean rate of switchings and arbitrary intensity of white Gaussian noise. We find the area at parameters plane where acceleration of diffusion in comparison with the free diffusion case takes place.
Variational methods for the steady state response of elastic–plastic solids subjected to cyclic loads
2003
Abstract Solids (or structures) of elastic–plastic internal variable material models and subjected to cyclic loads are considered. A minimum net resistant power theorem, direct consequence of the classical maximum intrinsic dissipation theorem of plasticity theory, is envisioned which describes the material behavior by determining the plastic flow mechanism (if any) corresponding to a given stress/hardening state. A maximum principle is provided which characterizes the optimal initial stress/hardening state of a cyclically loaded structure as the one such that the plastic strain and kinematic internal variable increments produced over a cycle are kinematically admissible. A steady cycle min…
Staged Venture Capital Contracting with Ratchets and Liquidation Rights
2011
Abstract This paper uses real options analysis to study later round financing in the presence of two standard venture capital contracting provisions: anti-dilution (ratchet) and liquidation preference. We argue that such provisions can preclude financing of a positive NPV venture in the case of a large follow-on financing relative to firm value. Liquidation preference contracting at multiples greater than one is not feasible in the later round if the financing is small relative to firm value. We highlight an interaction effect between the two provisions: increasing the liquidation multiple can help to avoid dilution and the need for the prior venture capitalist to waive ratchet provisions.
Evolution of small prokaryotic genomes
2015
As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokar…
Electrical Pumping of Potassium Ions Against an External Concentration Gradient in a Biological Ion Channel
2013
We show experimentally and theoretically that significant currents can be obtained with a biological ion channel, the OmpF porin of Escherichia coli, using zero-average potentials as driving forces. The channel rectifying properties can be used to pump potassium ions against an external concentration gradient under asymmetric pH conditions. The results are discussed in terms of the ionic selectivity and rectification ratio of the channel. The physical concepts involved may be applied to separation processes with synthetic nanopores and to bioelectrical phenomena. (C) 2013 AIP Publishing LLC.
Single-layer metal-on-metal islands driven by strong time-dependent forces
2012
Non-linear transport properties of single-layer metal-on-metal islands driven with strong static and time-dependent forces are studied. We apply a semi-empirical lattice model and use master equation and kinetic Monte Carlo simulation methods to compute observables such as the velocity and the diffusion coefficient. Two types of time-dependent driving are considered: a pulsed rotated field and an alternating field with a zero net force (electrophoretic ratchet). Small islands up to 12 atoms were studied in detail with the master equation method and larger ones with simulations. Results are presented mainly for a parametrization of Cu on Cu(001) surface, which has been the main system of int…
Small genomes and the difficulty to define minimal translation and metabolic machineries
2015
The notion of minimal life has sparked the interest of scientists in different fields, ranging from the origin-of-life research to biotechnology-oriented synthetic biology. Whether the interest is focused on the emergence of protocells out of prebiotic systems or the design of a cell chassis ready to incorporate new devices and functions, proposing minimal combinations of genes for life is not a trivial task. Using comparative genomics and biochemistry of endosymbionts (i.e., intracellular mutualistic symbionts) and intracellular parasites, a decade ago we proposed the core of a minimal gene set for a simple heterotrophic cell adapted to a chemically complex environment. In this work, we di…
Genetic lesions associated with Muller's ratchet in an RNA virus
1996
The molecular basis of Muller's ratchet has been investigated using the important animal pathogen foot-and-mouth disease virus (FMDV). Clones from two FMDV populations were subjected to serial plaque transfers (repeated bottleneck events) on host BHK-21 cells. Relative fitness losses were documented in 11 out of 19 clones tested. Small fitness gains were observed in three clones. One viral clone attained an extremely low plating efficiency, suggesting that accumulation of deleterious mutations had driven the virus near extinction. Nucleotide sequence analysis revealed unique genetic lesions in multiply transferred clones that had never been seen in FMDVs isolated in nature or subjected to m…
Initial state dependence of a quantum-resonance ratchet
2016
We demonstrate quantum resonance ratchets created with Bose-Einstein condensates exposed to pulses of an off-resonant standing light wave. We show how some of the basic properties of the ratchets are controllable through the creation of different initial states of the system. In particular, our results prove that through an appropriate choice of initial state it is possible to reduce the extent to which the ratchet state changes with respect to time. We develop a simple theory to explain our results and indicate how ratchets might be used as part of a matter wave interferometer or quantum-random walk experiment.