arXiv subjects
Publications and source records attributed to Arvind Murugan.
This is a copy of the 2009 Princeton University thesis which examined various aspects of gauge/gravity duality, including renormalization group flows, phase transitions of the holographic entanglement entropy, and instabilities associated with the breaking of supersymmetry. Chapter 5 contains new unpublished material on various instabilities of the weakly curved non-supersymmetric $AdS_4$ backgrounds of M-theory.
Non-equilibrium driving of biochemical reactions is believed to enable their robust functioning despite the presence of thermal fluctuations and other sources of disorder. Such robust functions include sensory adaptation, enhanced enyzmatic specificity and maintenance of coherent oscillations. Non-equilibrium biochemical reactions can be modeled as a master equation whose rate constants break detailed balance. We find that non equilibrium fluxes can support topologically protected boundary modes that resemble similar modes in electronic and mechanical systems. We show that when a biochemical network can be decomposed into two ordered bulks that meet at a possibly disordered interferace, the ordered bulks can be each associated with a topologically invariant winding number. If the winding numbers are mismatched, we are guaranteed that the steady state distribution is localized at the interface between the bulks, even in the presence of strong disorder in reaction rates. We argue that our work provides a framework for how biochemical systems can use non equilibrium driving to achieve robust function.
Specific interactions are a hallmark feature of self-assembly and signal-processing systems in both synthetic and biological settings. Specificity between components may arise from a wide variety of physical and chemical mechanisms in diverse contexts, from DNA hybridization to shape-sensitive depletion interactions. Despite this diversity, all systems that rely on interaction specificity operate under the constraint that increasing the number of distinct components inevitably increases off-target binding. Here we introduce `capacity', the maximal information encodable using specific interactions, to compare specificity across diverse experimental systems, and to compute how specificity changes with physical parameters. Using this framework, we find that `shape'-coding of interactions has higher capacity than chemical (`color') coding because the strength of off-target binding is strongly sublinear in binding site size for shapes while being linear for colors. We also find that different specificity mechanisms, such as shape and color, can be combined in a synergistic manner, giving a capacity greater than the sum of the parts.
Natural odors typically consist of many molecules at different concentrations. It is unclear how the numerous odorant molecules and their possible mixtures are discriminated by relatively few olfactory receptors. Using an information-theoretic model, we show that a receptor array is optimal for this task if it achieves two possibly conflicting goals: (i) each receptor should respond to half of all odors and (ii) the response of different receptors should be uncorrelated when averaged over odors presented with natural statistics. We use these design principles to predict statistics of the affinities between receptors and odorant molecules for a broad class of odor statistics. We also show that optimal receptor arrays can be tuned to either resolve concentrations well or distinguish mixtures reliably. Finally, we use our results to predict properties of experimentally measured receptor arrays. Our work can thus be used to better understand natural olfaction and it also suggests ways to improve artificial sensor arrays.
Biology achieves novel functions like error correction, ultra-sensitivity and accurate concentration measurement at the expense of free energy through Maxwell Demon-like mechanisms. The design principles and free energy trade-offs have been studied for a variety of such mechanisms. In this review, we emphasize a perspective based on dynamical phases that can explain commonalities shared by these mechanisms. Dynamical phases are defined by typical trajectories executed by non-equilibrium systems in the space of internal states. We find that coexistence of dynamical phases can have dramatic consequences for function vs free energy cost trade-offs. Dynamical phases can also provide an intuitive picture of the design principles behind such biological Maxwell Demons.
Self-assembly materials are traditionally designed so that molecular or meso-scale components form a single kind of large structure. Here, we propose a scheme to create "multifarious assembly mixtures", which self-assemble many different large structures from a set of shared components. We show that the number of multifarious structures stored in the solution of components increases rapidly with the number of different types of components. Yet, each stored structure can be retrieved by tuning only a few parameters, the number of which is only weakly dependent on the size of the assembled structure. Implications for artificial and biological self-assembly are discussed.
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change in its energy. In biological contexts, higher sensitivity corresponds to stronger discrimination between molecular substrates with different energetics competing in the same reaction. We study this discriminatory ability in systems with discrete states that are connected by a general network of transitions. We find multiple regimes of different discriminatory ability when the energy of a given state of the network is varied. Interestingly, the occupancy of the state can even increase with its energy, corresponding to an "anti-proofreading" regime. The number and properties of such discriminatory regimes are limited by the topology of the network. Finally, we find that discriminatory regimes can be changed without modifying any "hard-wired" structural aspects of the system but rather by simply changing external chemical potentials.
We use group theoretic methods to calculate the spectrum of short multiplets around the extremum of N=8 gauged supergravity potential which possesses N=2 supersymmetry and SU(3) global symmetry. Upon uplifting to M-theory, it describes a warped product of AdS_4 and a certain squashed and stretched 7-sphere. We find quantum numbers in agreement with those of the gauge invariant operators in the N=2 superconformal Chern-Simons theory recently proposed to be the dual of this M-theory background. This theory is obtained from the U(N)xU(N) theory through deforming the superpotential by a term quadratic in one of the superfields. To construct this model explicitly, one needs to employ monopole operators whose complete understanding is still lacking. However, for the U(2)xU(2) gauge theory we make a proposal for the form of the monopole operators which has a number of desired properties. In particular, this proposal implies enhanced symmetry of the U(2)xU(2) ABJM theory for k=1,2; it makes its similarity to and subtle difference from the BLG theory quite explicit.
We investigate the entanglement entropy in gravity duals of confining large $N_c$ gauge theories using the proposal of arXiv:hep-th/0603001, arXiv:hep-th/0605073. Dividing one of the directions of space into a line segment of length $l$ and its complement, the entanglement entropy between the two subspaces is given by the classical action of the minimal bulk hypersurface which approaches the endpoints of the line segment at the boundary. We find that in confining backgrounds there are generally two such surfaces. One consists of two disconnected components localized at the endpoints of the line segment. The other contains a tube connecting the two components. The disconnected surface dominates the entropy for $l$ above a certain critical value $l_{\rm crit}$ while the connected one dominates below that value. The change of behavior at $l=l_{\rm crit}$ is reminiscent of the finite temperature deconfinement transition: for $l < l_{\rm crit}$ the entropy scales as $N_c^2$, while for $l > l_{\rm crit}$ as $N_c^0$. We argue that a similar transition should occur in any field theory with a Hagedorn spectrum of non-interacting bound states. The requirement that the entanglement entropy has a phase transition may be useful in constraining gravity duals of confining theories.
We study supergravity backgrounds encoded through the gauge/string correspondence by the SU(N) \times SU(N) theory arising on N D3-branes on the conifold. As discussed in hep-th/9905104, the dynamics of this theory describes warped versions of both the singular and the resolved conifolds through different (symmetry breaking) vacua. We construct these supergravity solutions explicitly and match them with the gauge theory with different sets of vacuum expectation values of the bi-fundamental fields A_1, A_2, B_1, B_2. For the resolved conifold, we find a non-singular SU(2)\times U(1)\times U(1) symmetric warped solution produced by a stack of D3-branes localized at a point on the blown-up 2-sphere. It describes a smooth RG flow from AdS_5 \times T^{1,1} in the UV to AdS_5 \times S^5 in the IR, produced by giving a VEV to just one field, e.g. B_2. The presence of a condensate of baryonic operator det B_2 is confirmed using a Euclidean D3-brane wrapping a 4-cycle inside the resolved conifold. The Green's functions on the singular and resolved conifolds are central to our calculations and are discussed in some detail.
We study the potential governing D3-brane motion in a warped throat region of a string compactification with internal fluxes and wrapped D-branes. If the Kahler moduli of the compact space are stabilized by nonperturbative effects, a D3-brane experiences a force due to its interaction with D-branes wrapping certain four-cycles. We compute this interaction, as a correction to the warped four-cycle volume, using explicit throat backgrounds in supergravity. This amounts to a closed-string channel computation of the loop corrections to the nonperturbative superpotential that stabilizes the volume. We demonstrate for warped conical spaces that the superpotential correction is given by the embedding equation specifying the wrapped four-cycle, in agreement with the general form proposed by Ganor. Our approach automatically provides a solution to the problem of defining a holomorphic gauge coupling on wrapped D7-branes in a background with D3-branes. Finally, our results have applications to cosmological inflation models in which the inflaton is modeled by a D3-brane moving in a warped throat.
We study the fatgraph expansion for the Complex Matrix Quantum Mechanics (CMQM) with a Chern-Simons coupling. In the double-scaling limit this model is believed to describe Type 0A superstrings in 1+1 dimensions in a Ramond-Ramond electric field. With Euclidean time compactified, we show that the RR electric field acts as a chemical potential for vortices living on the Feynman diagrams of the CMQM. We interpret it as evidence that the CMQM Feynman diagrams discretize the NSR formulation of the noncritical Type 0A superstring. We also study T-duality for the CMQM diagrams and propose that a certain complex matrix model is dual to the noncritical Type 0B superstring.