On entropy production in the Madelung fluid and the role of Bohm's potential in classical diffusion

The Madelung equations map the non-relativistic time-dependent Schrodinger equation into hydrodynamic equations of a virtual fluid. Here we show that an increase of the Boltzmann entropy of this Madelung fluid is proportional to the expectation value of its velocity divergence. Hence, entropy growth is accompanied by expansion resulting from the ability of the Madelung fluid to be compressible. The compressibility itself reflects superposition of solutions of the Schrodinger equation. Thus, in unitary processes where the Madelung fluid expands and then shrinks, the Boltzmann entropy may, correspondingly, grow and then decrease. The notion of entropy growth due to expansion is common in diffusive processes, however in the latter the process is irreversible. Much unlike the Boltzmann entropy, the von Neumann entropy, does not vary with time. To elucidate the physical underpinning of the Boltzmann entropy, we examine several specific examples. We demonstrate that, for classical diffusive processes, the "force" accelerating diffusion has the form of the positive gradient of the quantum Bohm potential. In the Madelung fluid, the advective and the diffusive velocities correspond respectively to the the real and imaginary parts of the complex momentum. We find that the diffusion coefficient provides a lower bound of Heisenberg uncertainty type product between the gas mean free path and the Brownian momentum.Comment: 9 pages. The second version contains more examples and explanation

Evolutionary conservation of domain-domain interactions

BACKGROUND: Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs. RESULTS: Here we map structurally derived DDIs onto the cellular PPI networks of different organisms and demonstrate that there is a catalog of domain pairs that is used to mediate various interactions in the cell. We show that these DDIs occur frequently in protein complexes and that homotypic interactions (of a domain with itself) are abundant. A comparison of the repertoires of DDIs in the networks of Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens shows that many DDIs are evolutionarily conserved. CONCLUSION: Our results indicate that different organisms use the same 'building blocks' for PPIs, suggesting that the functionality of many domain pairs in mediating protein interactions is maintained in evolution

Dual-pump push-pull polarization control using stimulated Brillouin scattering

Stimulated Brillouin scattering (SBS) amplification of probe signals is highly polarization dependent. Maximum and minimum gain values are associated with a pair of orthogonal states of polarization (SOP), which are related to the pump SOP. Since the maximum gain is much higher than the minimum, the SOP of the output probe is pulled towards that of the maximum amplification. Polarization pulling is restricted, however, by pump depletion. In this work, a new method is proposed, analyzed and demonstrated for enhanced SBS polarization pulling, using two orthogonal pumps. Here, one pump amplifies one polarization component of the probe wave, and at the same time the other pump attenuates the corresponding orthogonal component, resulting in a push-pull effect. In the undepleted regime and for equal total power, the same degree of pulling is achieved as in the single pump case, but at a significantly less signal gain. Thus, the dual pump technique can provide high pulling efficiency for stronger input signals, deferring the onset of depletion

Polarization pulling based on stimulated Brillouin scattering in a dual-pump configuration

Stimulated Brillouin scattering (SBS) amplification of probe signals is highly polarization dependent. Maximum and minimum gain values are associated with a pair of orthogonal states of polarization (SOP) at the fiber output. Since the maximum gain is much higher than the minimum, the output probe SOP is pulled towards that of the maximum amplification. Polarization pulling is restricted, however, by pump depletion. In this work, we propose, analyze and demonstrate a method for enhanced SBS polarization pulling, using two orthogonal pumps: the one amplifies the probe wave whereas the other attenuates it. The method provides the same polarization pulling as that of a single amplifying pump, however it is considerably more tolerant to depletion

A Novel Translocation Breakpoint within the BPTF Gene Is Associated with a Pre-Malignant Phenotype

Partial gain of chromosome arm 17q is an abundant aberrancy in various cancer types such as lung and prostate cancer with a prominent occurrence and prognostic significance in neuroblastoma – one of the most common embryonic tumors. The specific genetic element/s in 17q responsible for the cancer-promoting effect of these aberrancies is yet to be defined although many genes located in 17q have been proposed to play a role in malignancy. We report here the characterization of a naturally-occurring, non-reciprocal translocation der(X)t(X;17) in human lung embryonal-derived cells following continuous culturing. This aberrancy was strongly correlated with an increased proliferative capacity and with an acquired ability to form colonies in vitro. The breakpoint region was mapped by fluorescence in situ hybridization (FISH) to the 17q24.3 locus. Further characterization by a custom-made comparative genome hybridization array (CGH) localized the breakpoint within the Bromodomain PHD finger Transcription Factor gene (BPTF), a gene involved in transcriptional regulation and chromatin remodeling. Interestingly, this translocation led to elevation in the mRNA levels of the endogenous BPTF. Knock-down of BPTF restricted proliferation suggesting a role for BPTF in promoting cellular growth. Furthermore, the BPTF chromosomal region was found to be amplified in various human tumors, especially in neuroblastomas and lung cancers in which 55% and 27% of the samples showed gain of 17q24.3, respectively. Additionally, 42% percent of the cancer cell lines comprising the NCI-60 had an abnormal BPTF locus copy number. We suggest that deregulation of BPTF resulting from the translocation may confer the cells with the observed cancer-promoting phenotype and that our cellular model can serve to establish causality between 17q aberrations and carcinogenesis

A Dynamic View of Domain-Motif Interactions

Many protein-protein interactions are mediated by domain-motif interaction, where a domain in one protein binds a short linear motif in its interacting partner. Such interactions are often involved in key cellular processes, necessitating their tight regulation. A common strategy of the cell to control protein function and interaction is by post-translational modifications of specific residues, especially phosphorylation. Indeed, there are motifs, such as SH2-binding motifs, in which motif phosphorylation is required for the domain-motif interaction. On the contrary, there are other examples where motif phosphorylation prevents the domain-motif interaction. Here we present a large-scale integrative analysis of experimental human data of domain-motif interactions and phosphorylation events, demonstrating an intriguing coupling between the two. We report such coupling for SH3, PDZ, SH2 and WW domains, where residue phosphorylation within or next to the motif is implied to be associated with switching on or off domain binding. For domains that require motif phosphorylation for binding, such as SH2 domains, we found coupled phosphorylation events other than the ones required for domain binding. Furthermore, we show that phosphorylation might function as a double switch, concurrently enabling interaction of the motif with one domain and disabling interaction with another domain. Evolutionary analysis shows that co-evolution of the motif and the proximal residues capable of phosphorylation predominates over other evolutionary scenarios, in which the motif appeared before the potentially phosphorylated residue, or vice versa. Our findings provide strengthening evidence for coupled interaction-regulation units, defined by a domain-binding motif and a phosphorylated residue