194 research outputs found
Insights into the relation between noise and biological complexity
Understanding under which conditions the increase of systems complexity is
evolutionary advantageous, and how this trend is related to the modulation of
the intrinsic noise, are fascinating issues of utmost importance for synthetic
and systems biology. To get insights into these matters, we analyzed chemical
reaction networks with different topologies and degrees of complexity,
interacting or not with the environment. We showed that the global level of
fluctuations at the steady state, as measured by the sum of the Fano factors of
the number of molecules of all species, is directly related to the topology of
the network. For systems with zero deficiency, this sum is constant and equal
to the rank of the network. For higher deficiencies, we observed an increase or
decrease of the fluctuation levels according to the values of the reaction
fluxes that link internal species, multiplied by the associated stoichiometry.
We showed that the noise is reduced when the fluxes all flow towards the
species of higher complexity, whereas it is amplified when the fluxes are
directed towards lower complexity species.Comment: 5 pages, 3 figure
Homotopy, monopoles and 't Hooft tensor in QCD with generic gauge group
We study monopoles and corresponding 't Hooft tensor in QCD with a generic
compact gauge group. This issue is relevant to the understanding of color
confinement in terms of dual symmetry.Comment: 15 pages. Accepted for publication in JHE
Supersymmetric Wilson loops at two loops
We study the quantum properties of certain BPS Wilson loops in
supersymmetric Yang-Mills theory. They belong to a general family, introduced
recently, in which the addition of particular scalar couplings endows generic
loops on with a fraction of supersymmetry. When restricted to ,
their quantum average has been further conjectured to be exactly computed by
the matrix model governing the zero-instanton sector of YM on the sphere.
We perform a complete two-loop analysis on a class of cusped Wilson loops lying
on a two-dimensional sphere, finding perfect agreement with the conjecture. The
perturbative computation reproduces the matrix-model expectation through a
highly non-trivial interplay between ladder diagrams and self-energies/vertex
contributions, suggesting the existence of a localization procedure.Comment: 35 pages, 14 figures, typos corrected, references adde
Deciphering noise amplification and reduction in open chemical reaction networks
The impact of random fluctuations on the dynamical behavior a complex
biological systems is a longstanding issue, whose understanding would shed
light on the evolutionary pressure that nature imposes on the intrinsic noise
levels and would allow rationally designing synthetic networks with controlled
noise. Using the It\=o stochastic differential equation formalism, we performed
both analytic and numerical analyses of several model systems containing
different molecular species in contact with the environment and interacting
with each other through mass-action kinetics. These systems represent for
example biomolecular oligomerization processes, complex-breakage reactions,
signaling cascades or metabolic networks. For chemical reaction networks with
zero deficiency values, which admit a detailed- or complex-balanced steady
state, all molecular species are uncorrelated. The number of molecules of each
species follow a Poisson distribution and their Fano factors, which measure the
intrinsic noise, are equal to one. Systems with deficiency one have an
unbalanced non-equilibrium steady state and a non-zero S-flux, defined as the
flux flowing between the complexes multiplied by an adequate stoichiometric
coefficient. In this case, the noise on each species is reduced if the flux
flows from the species of lowest to highest complexity, and is amplified is the
flux goes in the opposite direction. These results are generalized to systems
of deficiency two, which possess two independent non-vanishing S-fluxes, and we
conjecture that a similar relation holds for higher deficiency systems
CoCoNet—boosting RNA contact prediction by convolutional neural networks
Co-evolutionary models such as direct coupling analysis (DCA) in combination with machine learning (ML) techniques based on deep neural networks are able to predict accurate protein contact or distance maps. Such information can be used as constraints in structure prediction and massively increase prediction accuracy. Unfortunately, the same ML methods cannot readily be applied to RNA as they rely on large structural datasets only available for proteins. Here, we demonstrate how the available smaller data for RNA can be used to improve prediction of RNA contact maps. We introduce an algorithm called CoCoNet that is based on a combination of a Coevolutionary model and a shallow Convolutional Neural Network. Despite its simplicity and the small number of trained parameters, the method boosts the positive predictive value (PPV) of predicted contacts by about 70% with respect to DCA as tested by cross-validation of about eighty RNA structures. However, the direct inclusion of the CoCoNet contacts in 3D modeling tools does not result in a proportional increase of the 3D RNA structure prediction accuracy. Therefore, we suggest that the field develops, in addition to contact PPV, metrics which estimate the expected impact for 3D structure modeling tools better. CoCoNet is freely available and can be found at https://github.com/KIT-MBS/coconet
Monopoles, abelian projection, and gauge invariance
A direct connection is proved between the Non-Abelian Bianchi
Identities(NABI), and the abelian Bianchi identities for the 't Hooft tensor.
As a consequence the existence of a non-zero magnetic current is related to the
violation of the NABI's and is a gauge-invariant property. The construction
allows to show that not all abelian projections can be used to expose monopoles
in lattice configurations: each field configuration with non-zero magnetic
charge identifies its natural projection, up to gauge transformations which
tend to unity at large distances. It is shown that the so-called
maximal-abelian gauge is a legitimate choice. It is also proved, starting from
the NABI, that monopole condensation is a physical gauge invariant phenomenon,
independent of the choice of the abelian projection.Comment: 9 pages, no figur
Exploring the Mechanism of Formation of Native-like and Precursor Amyloid Oligomers for the Native Acylphosphatase from Sulfolobus solfataricus
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Femoral artery ultrasound examination: a new role in predicting cardiovascular risk
We compared intima-media thickness (IMT) and the prevalence of plaques in the common carotid artery (CCA) and common femoral artery (CFA) in apparently healthy participants. This multicenter study included 322 participants (59.9% female; age 20-78 years, mean 52.1 ± 15.3 years) who underwent Echo-color Doppler examination of the CCA and CFA bilaterally. Prevalence and composition of plaque were recorded. A significant ( P < .01) difference between mean CCA-IMT and mean CFA-IMT was detected (0.70 vs 0.73 mm). Plaque prevalence was significantly higher in the CFA compared to the CCA (40.7% vs 30.4%). Atherosclerotic plaques were found in both CFA and CCA in 46% of the cases, solely in CFA in 38%, and in CCA alone in 17%. The observed difference in plaque prevalence was even greater when only fibrolipid isolated plaques were considered (CFA 39.4% vs CCA 22.1%). In a healthy general population, atherosclerotic plaques were present in the CFA but not in the CCA in over one-third of the cases. Further studies must confirm whether ultrasonography of the CFA might be introduced in the screening protocols for cardiovascular risk assessment
Correlators of supersymmetric Wilson-loops, protected operators and matrix models in N=4 SYM
We study the correlators of a recently discovered family of BPS Wilson loops
in supersymmetric U(N) Yang-Mills theory. When the contours lie on
a two-sphere in the space-time, we propose a closed expression that is valid
for all values of the coupling constant and for any rank , by exploiting
the suspected relation with two-dimensional gauge theories. We check this
formula perturbatively at order for two latitude Wilson loops
and we show that, in the limit where one of the loops shrinks to a point,
logarithmic corrections in the shrinking radius are absent at .
This last result strongly supports the validity of our general expression and
suggests the existence of a peculiar protected local operator arising in the
OPE of the Wilson loop. At strong coupling we compare our result to the string
dual of the SYM correlator in the limit of large separation,
presenting some preliminary evidence for the agreement.Comment: 20 page, 8 figure
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