Black Branes in a Box: Hydrodynamics, Stability, and Criticality

We study the effective hydrodynamics of neutral black branes enclosed in a finite cylindrical cavity with Dirichlet boundary conditions. We focus on how the Gregory-Laflamme instability changes as we vary the cavity radius R. Fixing the metric at the cavity wall increases the rigidity of the black brane by hindering gradients of the redshift on the wall. In the effective fluid, this is reflected in the growth of the squared speed of sound. As a consequence, when the cavity is smaller than a critical radius the black brane becomes dynamically stable. The correlation with the change in thermodynamic stability is transparent in our approach. We compute the bulk and shear viscosities of the black brane and find that they do not run with R. We find mean-field theory critical exponents near the critical point.Comment: 23 pages, 3 figures. v2: added comments on first-order phase transitio

Hydrodynamics from charged black branes

We extend the recent work on fluid-gravity correspondence to charged black-branes by determining the metric duals to arbitrary charged fluid configuration up to second order in the boundary derivative expansion. We also derive the energy-momentum tensor and the charge current for these configurations up to second order in the boundary derivative expansion. We find a new term in the charge current when there is a bulk Chern-Simons interaction thus resolving an earlier discrepancy between thermodynamics of charged rotating black holes and boundary hydrodynamics. We have also confirmed that all our expressions are covariant under boundary Weyl-transformations as expected.Comment: 0+ 31 Pages; v2: 0+33 pages, typos corrected and new sections (in appendix) added; v3:published versio

Shock waves in strongly coupled plasmas

Shock waves are supersonic disturbances propagating in a fluid and giving rise to dissipation and drag. Weak shocks, i.e., those of small amplitude, can be well described within the hydrodynamic approximation. On the other hand, strong shocks are discontinuous within hydrodynamics and therefore probe the microscopics of the theory. In this paper we consider the case of the strongly coupled N=4 plasma whose microscopic description, applicable for scales smaller than the inverse temperature, is given in terms of gravity in an asymptotically $AdS_5$ space. In the gravity approximation, weak and strong shocks should be described by smooth metrics with no discontinuities. For weak shocks we find the dual metric in a derivative expansion and for strong shocks we use linearized gravity to find the exponential tail that determines the width of the shock. In particular we find that, when the velocity of the fluid relative to the shock approaches the speed of light $v\to 1$ the penetration depth $\ell$ scales as $\ell\sim (1-v^2)^{1/4}$. We compare the results with second order hydrodynamics and the Israel-Stewart approximation. Although they all agree in the hydrodynamic regime of weak shocks, we show that there is not even qualitative agreement for strong shocks. For the gravity side, the existence of shock waves implies that there are disturbances of constant shape propagating on the horizon of the dual black holes.Comment: 47 pages, 8 figures; v2:typos corrected, references adde

Nonlinear Hydrodynamics from Flow of Retarded Green's Function

We study the radial flow of retarded Green's function of energy-momentum tensor and $R$-current of dual gauge theory in presence of generic higher derivative terms in bulk Lagrangian. These are first order non-linear Riccati equations. We solve these flow equations analytically and obtain second order transport coefficients of boundary plasma. This way of computing transport coefficients has an advantage over usual Kubo approach. The non-linear equation turns out to be a linear first order equation when we study the Green's function perturbatively in momentum. We consider several examples including $Weyl^4$ term and generic four derivative terms in bulk. We also study the flow equations for $R$-charged black holes and obtain exact expressions for second order transport coefficients for dual plasma in presence of arbitrary chemical potentials. Finally we obtain higher derivative corrections to second order transport coefficients of boundary theory dual to five dimensional gauge supergravity.Comment: Version 2, reference added, typos correcte

Anisotropic Drag Force from 4D Kerr-AdS Black Holes

Using AdS/CFT we investigate the effect of angular-momentum-induced anisotropy on the instantaneous drag force of a heavy quark. The dual description is that of a string moving in the background of a Kerr-AdS black holes. The system exhibits the expected focussing of jets towards the impact parameter plane. We put forward that we can use the connection between this focussing behavior and the angular momentum induced pressure gradient to extrapolate the pressure gradient correction to the drag force that can be used for transverse elliptic flow in realistic RHIC. The result is recognizable as a relativistic pressure gradient force.Comment: 22 pages and 4 figure

Artificial Neural Network Inference (ANNI): A Study on Gene-Gene Interaction for Biomarkers in Childhood Sarcomas

Objective: To model the potential interaction between previously identified biomarkers in children sarcomas using artificial neural network inference (ANNI). Method: To concisely demonstrate the biological interactions between correlated genes in an interaction network map, only 2 types of sarcomas in the children small round blue cell tumors (SRBCTs) dataset are discussed in this paper. A backpropagation neural network was used to model the potential interaction between genes. The prediction weights and signal directions were used to model the strengths of the interaction signals and the direction of the interaction link between genes. The ANN model was validated using Monte Carlo cross-validation to minimize the risk of over-fitting and to optimize generalization ability of the model. Results: Strong connection links on certain genes (TNNT1 and FNDC5 in rhabdomyosarcoma (RMS); FCGRT and OLFM1 in Ewing’s sarcoma (EWS)) suggested their potency as central hubs in the interconnection of genes with different functionalities. The results showed that the RMS patients in this dataset are likely to be congenital and at low risk of cardiomyopathy development. The EWS patients are likely to be complicated by EWS-FLI fusion and deficiency in various signaling pathways, including Wnt, Fas/Rho and intracellular oxygen. Conclusions: The ANN network inference approach and the examination of identified genes in the published literature within the context of the disease highlights the substantial influence of certain genes in sarcomas

Thermodynamics and Instabilities of a Strongly Coupled Anisotropic Plasma

We extend our analysis of a IIB supergravity solution dual to a spatially anisotropic finite-temperature N=4 super Yang-Mills plasma. The solution is static, possesses an anisotropic horizon, and is completely regular. The full geometry can be viewed as a renormalization group flow from an AdS geometry in the ultraviolet to a Lifshitz-like geometry in the infrared. The anisotropy can be equivalently understood as resulting from a position-dependent theta-term or from a non-zero number density of dissolved D7-branes. The holographic stress tensor is conserved and anisotropic. The presence of a conformal anomaly plays an important role in the thermodynamics. The phase diagram exhibits homogeneous and inhomogeneous (i.e. mixed) phases. In some regions the homogeneous phase displays instabilities reminiscent of those of weakly coupled plasmas. We comment on similarities with QCD at finite baryon density and with the phenomenon of cavitation.Comment: 62 pages, 13 figures; v2: typos fixed, added reference

A novel class of microRNA-recognition elements that function only within open reading frames.

MicroRNAs (miRNAs) are well known to target 3' untranslated regions (3' UTRs) in mRNAs, thereby silencing gene expression at the post-transcriptional level. Multiple reports have also indicated the ability of miRNAs to target protein-coding sequences (CDS); however, miRNAs have been generally believed to function through similar mechanisms regardless of the locations of their sites of action. Here, we report a class of miRNA-recognition elements (MREs) that function exclusively in CDS regions. Through functional and mechanistic characterization of these 'unusual' MREs, we demonstrate that CDS-targeted miRNAs require extensive base-pairing at the 3' side rather than the 5' seed; cause gene silencing in an Argonaute-dependent but GW182-independent manner; and repress translation by inducing transient ribosome stalling instead of mRNA destabilization. These findings reveal distinct mechanisms and functional consequences of miRNAs that target CDS versus the 3' UTR and suggest that CDS-targeted miRNAs may use a translational quality-control-related mechanism to regulate translation in mammalian cells

Endoscopic sinus surgery for maxillary sinus mucoceles

BACKGROUND: Maxillary sinus mucoceles are relatively rare among all paranasal sinus mucoceles. With the introduction of endoscopic sinus surgical techniques, rhinologic surgeons prefer transnasal endoscopic management of sinus mucoceles. The aim of this study is to describe the clinical presentation of maxillary sinus mucoceles and to establish the efficacy of endoscopic management of sinus mucoceles. METHODS: Between 2003 and 2005, 14 patients underwent endoscopic sinus surgery for maxillary sinus mucocele. The presenting sign and symptoms, radiological findings, surgical management and need for revision surgery were reviewed. RESULTS: There were eight males and six females with an age range of 14 to 65. Ten patients complained of nasal obstruction, five of nasal drainage, five of cheek pressure or pain and one of proptosis of the eye and cheek swelling. The maxillary sinus and ipsilateral ethmoid sinus involvement on computed tomographic studies was seen in 4 patients. Four patients had history of endoscopic ethmoidectomy surgery for ethmoid sinusitis and one had Caldwell-Luc operation in the past. Ethmoidectomy with middle meatal antrostomy and marsupialization of the mucocele was performed in all patients. Postoperative follow-up ranged between 8 to 48 months. All patients had a patent middle meatal antrostomy and healthy maxillary sinus mucosa. No patients need revision surgery. CONCLUSION: The most common causes of mucoceles are chronic infection, allergic sinonasal disease, trauma and previous surgery. In 64% of the patients of our study cause remains uncertain. Endoscopic sinus surgery is an effective treatment for maxillary sinus mucoceles with a favorable long-term outcome

Enzyme sequestration as a tuning point in controlling response dynamics of signalling networks

Signalling networks result from combinatorial interactions among many enzymes and scaffolding proteins. These complex systems generate response dynamics that are often essential for correct decision-making in cells. Uncovering biochemical design principles that underpin such response dynamics is a prerequisite to understand evolved signalling networks and to design synthetic ones. Here, we use in silico evolution to explore the possible biochemical design space for signalling networks displaying ultrasensitive and adaptive response dynamics. By running evolutionary simulations mimicking different biochemical scenarios, we find that enzyme sequestration emerges as a key mechanism for enabling such dynamics. Inspired by these findings, and to test the role of sequestration, we design a generic, minimalist model of a signalling cycle, featuring two enzymes and a single scaffolding protein. We show that this simple system is capable of displaying both ultrasensitive and adaptive response dynamics. Furthermore, we find that tuning the concentration or kinetics of the sequestering protein can shift system dynamics between these two response types. These empirical results suggest that enzyme sequestration through scaffolding proteins is exploited by evolution to generate diverse response dynamics in signalling networks and could provide an engineering point in synthetic biology applications