Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization

Individual mRNAs are translated by multiple ribosomes that initiate translation with a few seconds interval. The ribosome speed is codon dependant, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modelling the stochastic translation process as a traffic problem, we here analyze conditions and consequences of collisions and queuing. The model allowed us to determine the on-rate (0.8 to 1.1 initiations per sec) and the time (1 sec) the preceding ribosome occludes initiation for Escherichia coli lacZ mRNA in vivo. We find that ribosome collisions and queues are inevitable consequences of a stochastic translation mechanism that reduce the translation efficiency substantially on natural mRNAs. The cells minimize collisions by having its mRNAs being unstable and by a highly selected codon usage in the start of the mRNA. The cost of mRNA breakdown is offset by the concomitant increase in translational efficiency.Comment: 5 figures, 3 table

Control over few photon pulses by a time-periodic modulation of the photon-emitter coupling

We develop a Floquet scattering formalism for the description of quasistationary states of microwave photons in a one-dimensional waveguide interacting with a nonlinear cavity by means of a periodically modulated coupling. This model is inspired by the recent progress in engineering of tunable coupling schemes with superconducting qubits. We argue that our model can realize the quantum analogue of an optical chopper. We find strong periodic modulations of the transmission and reflection envelopes in the scattered few-photon pulses, including photon compression and blockade, as well as dramatic changes in statistics. Our theoretical analysis allows us to explain these non-trivial phenomena as arising from non-adiabatic memory effects.Comment: 12 pages, 6 figures. arXiv admin note: substantial text overlap with arXiv:1603.0549

On the nonlinear statistics of range image patches

In [A. B. Lee, K. S. Pedersen, and D. Mumford, Int. J. Comput. Vis., 54 (2003), pp. 83–103], the authors study the distributions of 3 × 3 patches from optical images and from range images. In [G. Carlsson, T. Ishkanov, V. de Silva, and A. Zomorodian, Int. J. Comput. Vis., 76 (2008), pp. 1–12], the authors apply computational topological tools to the data set of optical patches studied by Lee, Pedersen, and Mumford and find geometric structures for high density subsets. One high density subset is called the primary circle and essentially consists of patches with a line separating a light and a dark region. In this paper, we apply the techniques of Carlsson et al. to range patches. By enlarging to 5×5 and 7×7 patches, we find core subsets that have the topology of the primary circle, suggesting a stronger connection between optical patches and range patches than was found by Lee, Pedersen, and Mumford

A Faster-Than Relation for Semi-Markov Decision Processes

When modeling concurrent or cyber-physical systems, non-functional requirements such as time are important to consider. In order to improve the timing aspects of a model, it is necessary to have some notion of what it means for a process to be faster than another, which can guide the stepwise refinement of the model. To this end we study a faster-than relation for semi-Markov decision processes and compare it to standard notions for relating systems. We consider the compositional aspects of this relation, and show that the faster-than relation is not a precongruence with respect to parallel composition, hence giving rise to so-called parallel timing anomalies. We take the first steps toward understanding this problem by identifying decidable conditions sufficient to avoid parallel timing anomalies in the absence of non-determinism.Comment: In Proceedings QAPL 2019, arXiv:2001.0616

Are all the frames equally important?

In this work, we address the problem of measuring and predicting temporal video saliency - a metric which defines the importance of a video frame for human attention. Unlike the conventional spatial saliency which defines the location of the salient regions within a frame (as it is done for still images), temporal saliency considers importance of a frame as a whole and may not exist apart from context. The proposed interface is an interactive cursor-based algorithm for collecting experimental data about temporal saliency. We collect the first human responses and perform their analysis. As a result, we show that qualitatively, the produced scores have very explicit meaning of the semantic changes in a frame, while quantitatively being highly correlated between all the observers. Apart from that, we show that the proposed tool can simultaneously collect fixations similar to the ones produced by eye-tracker in a more affordable way. Further, this approach may be used for creation of first temporal saliency datasets which will allow training computational predictive algorithms. The proposed interface does not rely on any special equipment, which allows to run it remotely and cover a wide audience.Comment: CHI'20 Late Breaking Work

Non-adiabatic effects in periodically driven-dissipative open quantum systems

We present a general method to calculate the quasi-stationary state of a driven-dissipative system coupled to a transmission line (and more generally, to a reservoir) under periodic modulation of its parameters. Using Floquet's theorem, we formulate the differential equation for the system's density operator which has to be solved for a single period of modulation. On this basis we also provide systematic expansions in both the adiabatic and high-frequency regime. Applying our method to three different systems -- two- and three-level models as well as the driven nonlinear cavity -- we propose periodic modulation protocols of parameters leading to a temporary suppression of effective dissipation rates, and study the arising non-adiabatic features in the response of these systems.Comment: 12 pages, 8 figure

Timed Comparisons of Semi-Markov Processes

Semi-Markov processes are Markovian processes in which the firing time of the transitions is modelled by probabilistic distributions over positive reals interpreted as the probability of firing a transition at a certain moment in time. In this paper we consider the trace-based semantics of semi-Markov processes, and investigate the question of how to compare two semi-Markov processes with respect to their time-dependent behaviour. To this end, we introduce the relation of being "faster than" between processes and study its algorithmic complexity. Through a connection to probabilistic automata we obtain hardness results showing in particular that this relation is undecidable. However, we present an additive approximation algorithm for a time-bounded variant of the faster-than problem over semi-Markov processes with slow residence-time functions, and a coNP algorithm for the exact faster-than problem over unambiguous semi-Markov processes