Dynamics of Triangulations

We study a few problems related to Markov processes of flipping triangulations of the sphere. We show that these processes are ergodic and mixing, but find a natural example which does not satisfy detailed balance. In this example, the expected distribution of the degrees of the nodes seems to follow the power law $d^{-4}$

Irreversible and reversible modes of operation of deterministic ratchets

We discuss a problem of optimization of the energetic efficiency of a simple rocked ratchet. We concentrate on a low-temperature case in which the particle's motion in a ratchet potential is deterministic. We show that the energetic efficiency of a ratchet working adiabatically is bounded from above by a value depending on the form of ratchet potential. The ratchets with strongly asymmetric potentials can achieve ideal efficiency of unity without approaching reversibility. On the other hand we show that for any form of the ratchet potential a set of time-protocols of the outer force exist under which the operation is reversible and the ideal value of efficiency is also achieved. The mode of operation of the ratchet is still quasistatic but not adiabatic. The high values of efficiency can be preserved even under elevated temperatures

The Cochlear Tuning Curve

The tuning curve of the cochlea measures how large an input is required to elicit a given output level as a function of the frequency. It is a fundamental object of auditory theory, for it summarizes how to infer what a sound was on the basis of the cochlear output. A simple model is presented showing that only two elements are sufficient for establishing the cochlear tuning curve: a broadly tuned traveling wave, moving unidirectionally from high to low frequencies, and a set of mechanosensors poised at the threshold of an oscillatory (Hopf) instability. These two components suffice to generate the various frequency-response regimes which are needed for a cochlear tuning curve with a high slope

Purulent vaginal discharge in grazing dairy cows: risk factors, reproductive performance, and prostaglandin F2α treatment

The objectives of this study were to assess the association of a 4-point scale of vaginal discharge score (VDS) with time to pregnancy to define criteria for a practical case of purulent vaginal discharge (PVD) in dairy cows, to test the risk factors for PVD, and, finally, the effect of a dose of PGF2α on cure and reproductive performance. In experiment 1, grazing Holstein cows (n = 2,414) had their vaginal discharge scored at ∼32 d in milk (DIM) on a 4-point scale, the effect of VDS on the hazard of pregnancy by 300 DIM was then assessed to derive a case definition of PVD. Risk factors for PVD and self-cure were also assessed. In experiment 2, grazing Holstein cows (n = 6,326) from 5 herds were checked for PVD at ∼30 DIM. Cows with PVD were assigned to receive one dose of 500 μg of PGF2α analog (Cloprostenol; Ciclase, Syntex SA, Buenos Aires, Argentina) per cow (odd ear tag number) or to remain untreated (even tag number). Cure was declared if cows presented clear normal vaginal discharge (VDS-0) at visit 2 (∼62 DIM). Data were analyzed with Cox's regression and mixed logistic models. In experiment 1, cows with VDS ≥1 had lower hazard of pregnancy and longer calving to pregnancy interval than cows with VDS-0. This finding was not affected by the time at which the diagnosis was performed. Therefore, a cow ≥21 DIM and having VDS ≥1 was used to define a case of PVD. The odds of PVD were greater in primiparous cows compared with multiparous, in cows with abnormal calving compared with those with normal calving, and in those losing BCS peripartum. In experiment 2, PGF2α treatment tended to slightly increase the hazard of pregnancy (adjusted hazard ratio = 1.13). Conversely, PGF2α had no effect on the odds of cure of PVD [adjusted odds ratio (AOR) = 1.19], pregnancy at first service (AOR = 1.03), or pregnancy by 100 DIM (AOR = 0.89) or 200 DIM (AOR = 1.27). In conclusion, cows with VDS ≥1 can be considered to have PVD because of their lower hazard of pregnancy and longer calving to pregnancy interval (up to 48 d). Important risk factors are parity, calving, and body condition score loss peripartum. Optimal time of diagnosis is ≥28 to 35 DIM because cows experience a high self-cure rate. Self-cure is also affected by parity, prepartum BCS, and VDS. Finally, as treatment with one dose of PGF2α had a small effect on the hazard of pregnancy and no effect on clinical cure, its therapeutic use in grazing dairy cows with PVD is not recommended.Facultad de Ciencias Veterinaria

Brownian Motors driven by Particle Exchange

We extend the Langevin dynamics so that particles can be exchanged with a particle reservoir. We show that grand canonical ensembles are realized at equilibrium and derive the relations of thermodynamics for processes between equilibrium states. As an application of the proposed evolution rule, we devise a simple model of Brownian motors driven by particle exchange. KEYWORDS: Langevin Dynamics, Thermodynamics, Open SystemsComment: 5 pages, late

Information and maximum power in a feedback controlled Brownian ratchet

Closed-loop or feedback controlled ratchets are Brownian motors that operate using information about the state of the system. For these ratchets, we compute the power output and we investigate its relation with the information used in the feedback control. We get analytical expressions for one-particle and few-particle flashing ratchets, and we find that the maximum power output has an upper bound proportional to the information. In addition, we show that the increase of the power output that results from changing the optimal open-loop ratchet to a closed-loop ratchet also has an upper bound that is linear in the information.Comment: LaTeX, 6 pages, 4 figures, improved version to appear in Eur. Phys. J.

Efficiency, selectivity and robustness of the nuclear pore complex transport

All materials enter or exit the cell nucleus through nuclear pore complexes (NPCs), efficient transport devices that combine high selectivity and throughput. A central feature of this transport is the binding of cargo-carrying soluble transport factors to flexible, unstructured proteinaceous filaments called FG-nups that line the NPC. We have modeled the dynamics of transport factors and their interaction with the flexible FG-nups as diffusion in an effective potential, using both analytical theory and computer simulations. We show that specific binding of transport factors to the FG-nups facilitates transport and provides the mechanism of selectivity. We show that the high selectivity of transport can be accounted for by competition for both binding sites and space inside the NPC, which selects for transport factors over other macromolecules that interact only non-specifically with the NPC. We also show that transport is relatively insensitive to changes in the number and distribution of FG-nups in the NPC, due mainly to their flexibility; this accounts for recent experiments where up to half of the total mass of the NPC has been deleted, without abolishing the transport. Notably, we demonstrate that previously established physical and structural properties of the NPC can account for observed features of nucleocytoplasmic transport. Finally, our results suggest strategies for creation of artificial nano-molecular sorting devices.Comment: 38 pages, six figure

Harshlight: a "corrective make-up" program for microarray chips

BACKGROUND: Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs), few tools are available to help with the detection of those defects. RESULTS: We develop a novel tool, Harshlight, for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify three different types of defects: localized blemishes affecting a few probes, diffuse defects affecting larger areas, and extended defects which may invalidate an entire chip. CONCLUSION: We demonstrate the use of Harshlight can materially improve analysis of HDONA chips, especially for experiments with subtle changes between samples. For the widely used MAS5 algorithm, we show that compact blemishes cause an average of 8 gene expression values per chip to change by more than 50%, two of them by more than twofold; our masking algorithm restores about two thirds of this damage. Large-scale artifacts are successfully detected and eliminated

Noise in neurons is message-dependent

Neuronal responses are conspicuously variable. We focus on one particular aspect of that variability: the precision of action potential timing. We show that for common models of noisy spike generation, elementary considerations imply that such variability is a function of the input, and can be made arbitrarily large or small by a suitable choice of inputs. Our considerations are expected to extend to virtually any mechanism of spike generation, and we illustrate them with data from the visual pathway. Thus, a simplification usually made in the application of information theory to neural processing is violated: noise {\sl is not independent of the message}. However, we also show the existence of {\sl error-correcting} topologies, which can achieve better timing reliability than their components.Comment: 6 pages,6 figures. Proceedings of the National Academy of Sciences (in press

Feynman's ratchet and pawl: an exactly solvable model

We introduce a simple, discrete model of Feynman's ratchet and pawl, operating between two heat reservoirs. We solve exactly for the steady-state directed motion and heat flows produced, first in the absence and then in the presence of an external load. We show that the model can act both as a heat engine and as a refrigerator. We finally investigate the behavior of the system near equilibrium, and use our model to confirm general predictions based on linear response theory.Comment: 19 pages + 10 figures; somewhat tighter presentatio