arXiv subjects

Marcelo O. Magnasco

Publications and source records attributed to Marcelo O. Magnasco.

28 records · Page 2Linked to original sources

arXiv2002

Solving the riddle of the bright mismatches: hybridization in oligonucleotide arrays

HDONA technology is predicated on two ideas. First, the differential between high-affinity (perfect match, PM) and lower-affinity (mismatch, MM) probes is used to minimize cross-hybridization. Second, several short probes along the transcript are combined, introducing redundancy. Both ideas have shown problems in practice: MMs are often brighter than PMs, and it is hard to combine the pairs because their brightness often spans decades. Previous analysis suggested these problems were sequence-related; publication of the probe sequences has permitted us an in-depth study of this issue. Our results suggest that fluorescently labeling the nucleotides interferes with mRNA binding, causing a catch-22 since, to be detected, the target mRNA must both glow and stick to its probe: without labels it cannot be seen even if bound, while with too many it won't bind. We show that this conflict causes much of the complexity of HDONA raw data, suggesting that an accurate physical understanding of hybridization by incorporating sequence information is necessary to perfect microarray analysis.

physics.bio-ph↗

arXiv2001

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.

physics.bio-ph↗

arXiv2001

Noise and Inertia-Induced Inhomogeneity in the Distribution of Small Particles in Fluid Flows

The dynamics of small spherical neutrally buoyant particulate impurities immersed in a two-dimensional fluid flow are known to lead to particle accumulation in the regions of the flow in which rotation dominates over shear, provided that the Stokes number of the particles is sufficiently small. If the flow is viewed as a Hamiltonian dynamical system, it can be seen that the accumulations occur in the nonchaotic parts of the phase space: the Kolmogorov--Arnold--Moser tori. This has suggested a generalization of these dynamics to Hamiltonian maps, dubbed a bailout embedding. In this paper we use a bailout embedding of the standard map to mimic the dynamics of impurities subject not only to drag but also to fluctuating forces modelled as white noise. We find that the generation of inhomogeneities associated with the separation of particle from fluid trajectories is enhanced by the presence of noise, so that they appear in much broader ranges of the Stokes number than those allowing spontaneous separation.

nlin.CD↗

arXiv2001

Bailout Embeddings, Targeting of KAM Orbits, and the Control of Hamiltonian Chaos

We present a novel technique, which we term bailout embedding, that can be used to target orbits having particular properties out of all orbits in a flow or map. We explicitly construct a bailout embedding for Hamiltonian systems so as to target KAM orbits. We show how the bailout dynamics is able to lock onto extremely small KAM islands in an ergodic sea.

nlin.CD↗

arXiv2001

Negative Resistance in Brownian Transport

We prove that negative incremental resistance cannot occur on 1D spaces like the circle or the line; we construct an explicit two-dimensional model on the cylinder, and its collapse into a branched 1D backbone. We derive an accurate numerical method for solving our 2D model, and discuss the relevance of the model to biological ion channels.

cond-mat.stat-mech↗

arXiv2001

Unsupervised learning and adaptation in a model of adult neurogenesis

Adult neurogenesis has long been documented in the vertebrate brain, and recently even in humans. Although it has been conjectured for many years that its functional role is related to the renewing of memories, no clear mechanism as to how this can be achieved has been proposed. We present a scheme in which incorporation of new neurons proceeds at a constant rate, while their survival is activity-dependent and thus contingent upon new neurons establishing suitable connections. We show that a simple mathematical model following these rules organizes its activity so as to maximize the difference between its responses, and can adapt to changing environmental conditions in unsupervised fashion.

cond-mat.dis-nn↗

arXiv2001

From features to expression: High-density oligonucleotide array analysis revisited

One of the most popular tools for large scale gene expression studies are high-density oligonucleotide (GeneChip(R)) arrays. These currently have 16-20 small probe cells (``features'') for evaluating the transcript abundance of each gene. In addition, each probe is accompanied by a mismatched probe designed as a control for non-specificity. An algorithm is presented to compute comparative expression levels from the intensities of the individual features, based on a statistical study of their distribution. Interestingly, MM probes need not be included in the analysis. We show that our algorithm improves significantly upon the current standard and leads to a substantially larger number of genes brought above the noise floor for further analysis.

physics.bio-ph↗

arXiv2000

The thunder of distant Net storms

Computers and routers on the Internet send each other error messages (called ICMP datagrams) to signal conditions such as network congestion or blackouts. While these datagrams are very rare, less than 0.001% of total traffic, they hold very important global information about problems and congestions elsewhere in the Net. A measurement of the flow of such error messages in our local cluster shows a very pathological distribution of inter-message times: $P(Δt) \approx 1/Δt$. This scaling extends for about seven decades, and is only punctuated by extraneously periodic signals from automatons. More than a half of these error messages were themselves generated erroneously.

nlin.AO↗

arXiv2000

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.

cond-mat.dis-nn↗

arXiv1999

Noise-induced memory in extended excitable systems

We describe a form of memory exhibited by extended excitable systems driven by stochastic fluctuations. Under such conditions, the system self-organizes into a state characterized by power-law correlations thus retaining long-term memory of previous states. The exponents are robust and model-independent. We discuss novel implications of these results for the functioning of cortical neurons as well as for networks of neurons.

adap-org↗