Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.
Until the 19th century, technology was essentially the domain of skilled artisans and constructors who relied on practical experience to design and build their machines. One of the first efforts to use physical theory to study the functioning of machines was undertaken by the French engineer Sadi Carnot. Motivated by the concern of the French about the superiority of British steam engines, he undertook a systematic study of the physical processes governing steam engines, resulting in his remarkable paper Reflexions sur la puissance motrice du feu (On the Motive Power of Heat) published in 1826. Among the earliest successes of this new science, thermodynamics, was the formulation of criteria describing how well real processes perform in comparison with an ideal model. Carnot showed that any engine, using heat from a hot reservoir at temperature Th to do work, has to transfer some heat to a reservoir at lower temperature T1, and that no engine could convert into work more of the heat taken in at Th than the fraction ηC = 1−(T1/Th) known as the Carnot efficiency.
The cornerstone of finite-time thermodynamics is all about the price of haste and how to minimize it. Reversible processes may be ultimately efficient, but they are unrealistically slow. In all situations-chemical, mechanical, economical-we pay extra to get the job done quickly. Finite-time thermodynamics can be used to develop methods to limit that extra expenditure, be it in energy, entropy production, money, or something entirely different. Finite-time thermodynamics also includes methods to calculate the optimal path or mode of operation to achieve this minimal expenditure. The concept is to place the system of interest in contact with a time-varying environment which will coax the system along the desired path, much like guiding a horse along by waving a carrot in front of it.
The proportionality between the square of the distance traversed as measured in thermodynamic length and the minimum associated dissipation of a process is established in a new context independent of dynamical laws. A quasistatic thermodynamic process consisting of K steps, each equilibrating with an appropriate reservoir, is optimized with respect to the position of the steps and the allocation of the total time τ for the process among the steps. It is found that the steps should be of equal thermodynamic length. For large K the bounds based on thermodynamic length are recovered.
Using computer experiments on a simple three-state system and an NP-complete system of permanents we compare different proposed simulated annealing schedules in order to find the cooling strategy which has the least total entropy production during the annealing process for given initial and final states and fixed number of iterations. The schedules considered are constant thermodynamic speed, exponential, logarithmic, and linear cooling schedules. The constant thermodynamic speed schedule is shown to be the best. We are actually considering two different schedules with constant thermodynamic speed, the original one valid for nearequilibrium processes, and a version based on the natural timescale valid also at higher speeds. The latter one delivers better results, especially in case of fast cooling or when the system is far from equilibrium. Also with the lowest energy encountered during the entire optimization (the best-so-far-energy) as the indicator of merit, constant thermodynamic speed is superior. Finally, we have compared two different estimators of the relaxation time. One estimator is using the second largest eigenvalue of the thermalized form of the transition probability matrix and the other is using a simpler approximation for small deviations from equilibrium. These two different expressions only agree at high temperatures.
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