Entropy driven key-lock assembly

The effective interaction between a sphere with an open cavity (lock) and a spherical macroparticle (key), both immersed in a hard sphere fluid, is studied by means of Monte Carlo simulations. As a result, a 2d map of the key-lock effective interaction potential is constructed, which leads to the proposal of a self-assembling mechanism: there exists trajectories through which the key-lock pair could assemble avoiding trespassing potential barriers. Hence, solely the entropic contribution can induce their self-assembling even in the absence of attractive forces. This study points out the solvent contribution within the underlying mechanisms of substrate-protein assembly/disassembly processes, which are important steps of the enzyme catalysis and protein mediated transport

Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics

Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems the inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems, their basic properties allow to understand fundamental dynamical properties of complex biological reaction networks. We analyze the Lyapunov spectrum, determine the probability to find stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network and study how the frequency distributions of oscillatory modes of such system depend on the average connectivity.Comment: 11 pages, 5 figure

A variety of Levitrons: A review

After a brief history and critique of some older instruments, several new Levitron geometries are described. As a result of their greater stability these devices can be used as analogues of a number of phenomena and applications, including magnetic resonance techniques, atom traps and accelerator rings. In particular, the notion of the spinning magnet (or spignet) in a linear trap is similar to the mechanism underpinning the confinement of antihydrogen in a magnetic minimum trap, as achieved in experiments at CERN

ASASSN-13db 2014-2017 Eruption as an Intermediate Luminosity Optical Transient

The low mass star ASASSN-13db experienced an EXor outburst in 2013, which identified it as a Young Stellar Object (YSO). Then, from 2014 to 2017 it had another outburst, longer and more luminous than the earlier. We analyze the observations of the second outburst, and compare it to eruptions of Intermediate Luminosity Optical Transients (ILOTs). We show that the decline of the light curve is almost identical to that of the V838 Mon, a prototype of a type of ILOT known as Luminous Red Nova (LRN). This similarity becomes conspicuous when oscillations that are associated with rotation are filtered out from the light curve of ASASSN-13db. We suggest that the eruption was the result of accretion of a proto-planet of a few Earth masses. The proto-planet was shredded by tidal forces before it was accreted onto the YSO, releasing gravitational energy that powered the outburst for $\approx 800$ days, and ended in a $\approx 55$ days decline phase. When the accretion material started depleting the accretion rate lowered and the eruption light curve declined for almost two months. Then it exhausted completely, creating a sharp break in the light curve. Another possibility is that the mass was a result of an instability in the proto-planetary disk that lead to a large episode of accretion from an inner viscous disk. We find that the variation of the temperature of the outburst is consistent with the surface temperature expected from a depleted viscous accretion disk. The 2014-2017 outburst of ASASSN-13db may be the least energetic ILOT to have been discovered to date, with an energy budget of only $\approx 10^{42}$ erg.Comment: Accepted to Galaxie

Gene Therapy Applications to Cancer Treatment

Over the past ten years significant advances have been made in the fields of gene therapy and tumour immunology, such that there now exists a considerable body of evidence validating the proof in the principle of gene therapy based cancer vaccines. While clinical benefit has so far been marginal, data from preclinical and early clinical trials of gene therapy combined with standard therapies are strongly suggestive of additional benefit. Many reasons have been proposed to explain the paucity of clinical responses to single agent vaccination strategies including the poor antigenicity of tumour cells and the development of tolerance through down-regulation of MHC, costimulatory, signal transduction, and other molecules essential for the generation of strong immune responses. In addition, there is now evidence from animal models that the growing tumour may actively inhibit the host immune response. Removal of the primary tumour prior to T cell transfer from the spleen of cancer bearing animals, led to effective tumour cell line specific immunity in the recipient mouse suggesting that there is an ongoing tumour-host interaction. This model also illustrates the potential difficulties of clinical vaccine trials in patients with advanced stage disease

Classification of All Poisson-Lie Structures on an Infinite-Dimensional Jet Group

A local classification of all Poisson-Lie structures on an infinite-dimensional group $G_{\infty}$ of formal power series is given. All Lie bialgebra structures on the Lie algebra {\Cal G}_{\infty} of $G_{\infty}$ are also classified.Comment: 11 pages, AmSTeX fil

Michaelis-Menten dynamics in protein subnetworks

To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past, and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain a description of subnetwork dynamics, including memory functions, starting directly from any given network of unary, binary and Michaelis-Menten reactions. Numerical tests show that this closed form enzyme elimination gives a much more accurate description of the subnetwork dynamics than the simpler method that represents enzymes explicitly, and is also more efficient computationally

Toward an ecological aesthetics: music as emergence

In this article we intend to suggest some ecological based principles to support the possibility of develop an ecological aesthetics. We consider that an ecological aesthetics is founded in concepts as “direct perception”, “acquisition of affordances and invariants”, “embodied embedded perception” and so on. Here we will purpose that can be possible explain especially soundscape music perception in terms of direct perception, working with perception of first hand (in a Gibsonian sense). We will present notions as embedded sound, detection of sonic affordances and invariants, and at the end we purpose an experience with perception/action paradigm to make soundscape music as emergence of a self-organized system

Oxaloacetate Enhances Neuronal Cell Bioenergetic Fluxes and Infrastructure

"This is the peer reviewed version of the following article: Wilkins, Heather M. et al. “Oxaloacetate Enhances Neuronal Cell Bioenergetic Fluxes and Infrastructure.” Journal of neurochemistry 137.1 (2016): 76–87., which has been published in final form at 10.1111/jnc.13545. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."We tested how the addition of oxaloacetate (OAA) to SH-SY5Y cells affected bioenergetic fluxes and infrastructure, and compared the effects of OAA to malate, pyruvate, and glucose deprivation. OAA displayed pro-glycolysis and pro-respiration effects. OAA pro-glycolysis effects were not a consequence of decarboxylation to pyruvate because unlike OAA, pyruvate lowered the glycolysis flux. Malate did not alter glycolysis flux and reduced mitochondrial respiration. Glucose deprivation essentially eliminated glycolysis and increased mitochondrial respiration. OAA increased, while malate decreased, the cell NAD+/NADH ratio. Cytosolic malate dehydrogenase 1 (MDH1) protein increased with OAA treatment, but not with malate or glucose deprivation. Glucose deprivation increased protein levels of ATP citrate lyase, an enzyme which produces cytosolic OAA, while OAA altered neither ATP citrate lyase mRNA nor protein levels. OAA, but not glucose deprivation, increased COX2, PGC1α, PGC1β, and PRC protein levels. OAA increased total and phosphorylated SIRT1 protein. We conclude that adding OAA to SH-SY5Y cells can support or enhance both glycolysis and respiration fluxes. These effects appear to depend, at least partly, on OAA causing a shift in the cell redox balance to a more oxidized state, that it is not a glycolysis pathway intermediate, and possibly its ability to act in an anaplerotic fashion