arXiv subjects

Dmitry Melnikov

Publications and source records attributed to Dmitry Melnikov.

36 records · Page 2Linked to original sources

arXiv2019

A Continuous Effective Model of the Protein Dynamics

The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins. In this letter we report a detailed study of the basic features of a version of the proposed model, which assumes proteins to be very long continuous curves. In the most appealing case, the model is based on a potential with a pair of minima corresponding to helical and strand-like configurations of the curves. It allows to derive several predictions about the geometric features of the molecules, and we show that the predictions are compatible with the phenomenology. While the helices represent the ground state configurations, the abundance of beta strands is controlled by a parameter, which can either completely suppress their presence in a molecule, or make them abundant. The few-parameter model investigated in the letter rather represents a universality class of protein molecules. Generalizations accounting for the discrete nature and inhomogeneity of the molecules presumably allow to model realistic cases.

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arXiv2019

Lifshitz Scaling, Microstate Counting from Number Theory and Black Hole Entropy

Non-relativistic field theories with anisotropic scale invariance in (1+1)-d are typically characterized by a dispersion relation $E\sim k^{z}$ and dynamical exponent $z>1$. The asymptotic growth of the number of states of these theories can be described by an extension of Cardy formula that depends on $z$. We show that this result can be recovered by counting the partitions of an integer into $z$-th powers, as proposed by Hardy and Ramanujan a century ago. This gives a novel relationship between the characteristic energy of the dispersion relation with the cylinder radius and the ground state energy. For free bosons with Lifshitz scaling, this relationship is shown to be identically fulfilled by virtue of the reflection property of the Riemann $ζ$-function. The quantum Benjamin-Ono$_{2}$ (BO$_{2}$) integrable system, relevant in the AGT correspondence, is also analyzed. As a holographic realization, we provide a special set of boundary conditions for which the reduced phase space of Einstein gravity with a couple of $U(1)$ fields on AdS$_3$ is described by the BO$_{2}$ equations. This suggests that the phase space can be quantized in terms of quantum BO$_{2}$ states. Indeed, in the semiclassical limit, the ground state energy of BO$_{2}$ coincides with the energy of global AdS$_{3}$, and the Bekenstein-Hawking entropy for BTZ black holes is recovered from the anisotropic extension of Cardy formula.

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arXiv2019

Circuit Complexity of Knot States in Chern-Simons theory

We compute an upper bound on the circuit complexity of quantum states in $3d$ Chern-Simons theory corresponding to certain classes of knots. Specifically, we deal with states in the torus Hilbert space of Chern-Simons that are the knot complements on the $3$-sphere of arbitrary torus knots. These can be constructed from the unknot state by using the Hilbert space representation of the $S$ and $T$ modular transformations of the torus as fundamental gates. The upper bound is saturated in the semiclassical limit of Chern-Simons theory. The results are then generalized for a family of multi-component links that are obtained by "Hopf-linking" different torus knots. We also use the braid word presentation of knots to discuss states on the punctured sphere Hilbert space associated with 2-bridge knots and links. The calculations present interesting number theoretic features related with continued fraction representations of rational numbers. In particular, we show that the minimization procedure defining the complexity naturally leads to regular continued fractions, allowing a geometric interpretation of the results in the Farey tesselation of the upper-half plane. Finally, we relate our discussion to the framework of path integral optimization by generalizing the original argument to non-trivial topologies.

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arXiv2019

Topological Indices of Proteins

Protein molecules can be approximated by discrete polygonal chains of amino acids. Standard topological tools can be applied to the smoothening of the polygons to introduce a topological classification of proteins, for example, using the self-linking number of the corresponding framed curves. In this paper we add new details to the standard classification. Known definitions of the self-linking number apply to non-singular framings: for example, the Frenet framing cannot be used if the curve has inflection points. Meanwhile in the discrete proteins the special points are naturally resolved. Consequently, a separate integer topological characteristics can be introduced, which takes into account the intrinsic features of the special points. For large number of proteins we compute integer topological indices associated with the singularities of the Frenet framing. We show how a version of the Calugareanu's theorem is satisfied for the associated self-linking number of a discrete curve. Since the singularities of the Frenet framing correspond to the structural motifs of proteins, we propose topological indices as a technical tool for the description of the folding dynamics of proteins.

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arXiv2017

Topological transport from a black hole

In this paper the low temperature zero-frequency transport in a 2+1-dimensional theory dual to a dyonic black hole is discussed. It is shown that transport exhibits topological features: the transverse electric and heat conductivities satisfy the Wiedemann-Franz law of free electrons; the direct heat conductivity is measured in units of the central charge of the dual CFT, while the direct electric conductivity vanishes; the thermoelectric conductivity is non-zero at vanishing temperature, while the linear in temperature behaviour, controlled by the Mott relation, is subleading. Provided that the entropy of the black hole, and the dual system, is non-vanishing at zero temperature, the observations indicate that the dyonic black hole describes a "classical" limit of a highly degenerate topological state, in which the black hole charge measures the density of excited non-abelian quasiparticles.

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arXiv2015

Chern-Simons Improved Hamiltonians for Strings in Three Space Dimensions

The Frenet equation governs the extrinsic geometry of a string in three-dimensional ambient space in terms of the curvature and torsion, which are both scalar functions under string reparameterisations. The description engages a local SO(2) gauge symmetry, which emerges from the invariance of the extrinsic string geometry under local frame rotations around the tangent vector. Here we inquire how to construct the most general SO(2) gauge invariant Hamiltonian of strings, in terms of the curvature and torsion. The construction instructs us to introduce a long-range (self-) interaction between strings, which is mediated by a three dimensional bulk gauge field with a Chern-Simons self-interaction. The results support the proposal that fractional statistics should be prevalent in the case of three dimensional string-like configurations.

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arXiv2015

Holographic Baryons and Instanton Crystals

In a wide class of holographic models, like the one proposed by Sakai and Sugimoto, baryons can be approximated by instantons of non-abelian gauge fields that live on the world-volume of flavor D-branes. In the leading order, those are just the Yang-Mills instantons, whose solutions can be obtained from the celebrated ADHM construction. This fact can be used to study various properties of baryons in the holographic limit. In particular, one can attempt to construct a holographic description of the cold dense nuclear matter phase of baryons. It can be argued that holographic baryons in such a regime are necessarily in a solid crystalline phase. In this review we summarize the known results on the construction and phases of crystals of the holographic baryons.

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arXiv2014

Matrix integral expansion of colored Jones polynomials for figure-eight knot

In this note we examine a possible extension of the matrix integral representation of knot invariants beyond the class of torus knots. In particular, we study a representation of the SU(2) quantum Racah coefficients by double matrix integrals. We find that the Racah coefficients are mapped to expansion coefficients in some basis of double integrals. The transformed coefficients have a number of interesting algebraic properties.

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arXiv2014

Black Holes in AdS/BCFT and Fluid/Gravity Correspondence

A proposal to describe gravity duals of conformal theories with boundaries (AdS/BCFT correspondence) was put forward by Takayanagi few years ago. However interesting solutions describing field theories at finite temperature and charge density are still lacking. In this paper we describe a class of theories with boundary, which admit black hole type gravity solutions. The theories are specified by stress-energy tensors that reside on the extensions of the boundary to the bulk. From this perspective AdS/BCFT appears analogous to the fluid/gravity correspondence. Among the class of the boundary extensions there is a special (integrable) one, for which the stress-energy tensor is fluid-like. We discuss features of that special solution as well as its thermodynamic properties.

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arXiv2013

Calculation of glueball spectra in supersymmetric theories via holography

Lattice simulations currently present the only way to access nonperturbative data in strongly coupled theories from a first principle calculation. However, in supersymmetric theories this valuable tool is not available due to the technical sign problem. We are going to demonstrate that in the case of glueball spectra a good quantitative estimate for the lightest states of low spin can be obtained by means of the holographic approach. We will review the results of the calculation in the singlet glueball sector of the N=1 supersymmetric Klebanov-Strassler model. We come up with a prediction of the spectrum of lightest glueballs in (large Nc) N=1 supersymmetric Yang-Mills theory.

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arXiv2012

Baryonic Popcorn

In the large N limit cold dense nuclear matter must be in a lattice phase. This applies also to holographic models of hadron physics. In a class of such models, like the generalized Sakai-Sugimoto model, baryons take the form of instantons of the effective flavor gauge theory that resides on probe flavor branes. In this paper we study the phase structure of baryonic crystals by analyzing discrete periodic configurations of such instantons. We find that instanton configurations exhibit a series of "popcorn" transitions upon increasing the density. Through these transitions normal (3D) lattices expand into the transverse dimension, eventually becoming a higher dimensional (4D) multi-layer lattice at large densities. We consider 3D lattices of zero size instantons as well as 1D periodic chains of finite size instantons, which serve as toy models of the full holographic systems. In particular, for the finite-size case we determine solutions of the corresponding ADHM equations for both a straight chain and for a 2D zigzag configuration where instantons pop up into the holographic dimension. At low density the system takes the form of an "abelian anti-ferromagnetic" straight periodic chain. Above a critical density there is a second order phase transition into a zigzag structure. An even higher density yields a rich phase space characterized by the formation of multi-layer zigzag structures. The finite size of the lattices in the transverse dimension is a signal of an emerging Fermi sea of quarks. We thus propose that the popcorn transitions indicate the onset of the "quarkyonic" phase of the cold dense nuclear matter.

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arXiv2012

On the AdS/BCFT Approach to Quantum Hall Systems

In this paper we study a simple gravity model dual to a (2+1)-dimensional system with a boundary at finite charge density and temperature. In our naive AdS/BCFT extension of a well known AdS/CFT system a non-zero charge density must be supported by a magnetic field. As a result, the Hall conductivity is a constant inversely proportional to the coefficients of pertinent topological terms. Since the direct conductivity vanishes, such behaviors resemble that of a quantum Hall system with Fermi energy in the gap between the Landau levels. We further analyze the properties stemming from our holographic approach to a quantum Hall system. We find that at low temperatures the thermal and electric conductivities are related through the Wiedemann-Franz law, so that every charge conductance mode carries precisely one quantum of the heat conductance. From the computation of the edge currents we learn that the naive holographic model is dual to a gapless system if tensionless RS branes are used in the AdS/BCFT construction. To reconcile this result with the expected quantum Hall behavior we conclude that gravity solutions with tensionless RS branes must be unstable, calling for a search of more general solutions. We briefly discuss the expected features of more realistic holographic setups.

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arXiv2010

Attractive Holographic Baryons

We propose a holographic model of baryon interactions based on non-supersymmetric D7-anti-D7 flavor branes embedded in the Klebanov-Strassler background. The baryons are D3-branes wrapping the 3-sphere of the conifold with M strings connecting the D3 and the flavor branes. Depending on the location of the latter there are two possibilities: the D3 either remains separate from the flavor branes or dissolves in them and becomes a flavor instanton. The leading order interaction between the baryons is a competition between the attraction and the repulsion due to the sigma and omega mesons. The lightest 0++ particle sigma is a pseudo-Goldstone boson associated with the spontaneous breaking of scale invariance. In a certain range of parameters it is parametrically lighter than any other massive state. As a result at large distances baryons attract each other. At short distances the potential admits a repulsive core due to an exchange of the omega vector meson. We discuss baryon coupling to glueballs, massive mesons and pions and point out the condition for the model to have a small binding energy.

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arXiv2009

On I-even Singlet Glueballs in the Klebanov-Strassler Theory

In this note we study vector fluctuations over the Klebanov-Strassler type IIB supergravity solution that are even under the I-conjugation. We are interested only in the states invariant under the global SU(2)x SU(2) symmetry. Apart from the glueball dual to the R-current there is one more 1++ state, which is a member of a massive vector multiplet containing also a scalar 0++. Combined with previous results, our analysis allows to complete the list of low energy singlet supermultiplets in the Klebanov-Strassler theory.

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arXiv2009

Stability of Asymptotically Schroedinger RN Black Hole and Superconductivity

We perform a perturbative (near-critical) analysis of the stability of an asymptotically Schroedinger Reissner-Nordstrom black hole with respect to generation of charged scalar hair. We find that apart from the expected instability at low temperatures typical of holographic models of superconductivity, in the presence of certain operators a similar instability appears as well at high temperatures. We propose that the reason for such a phase diagram could be due to peculiar features of the dual gauge theory or the failure of the model to provide a consistent holographic dual of a non-relativistic superconductor.

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arXiv2009

A Pure-Glue Hidden Valley I. States and Decays

It is possible that the standard model is coupled, through new massive charged or colored particles, to a hidden sector whose low energy dynamics is controlled by a pure Yang-Mills theory, with no light matter. Such a sector would have numerous metastable "hidden glueballs" built from the hidden gluons. These states would decay to particles of the standard model. We consider the phenomenology of this scenario, and find formulas for the lifetimes and branching ratios of the most important of these states. The dominant decays are to two standard model gauge bosons, or by radiative decays with photon emission, leading to jet- and photon-rich signals.

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arXiv2009

I-odd sector of the Klebanov-Strassler theory

The Klebanov-Strassler background is invariant under the Z_2 symmetry I, which acts by exchanging the bi-fundamental fields A and B, accompanied by the charge conjugation. We study the background perturbations in the I-odd sector and find an exhaustive list of bosonic states invariant under the global SU(2)*SU(2) symmetry. In addition to the scalars identified in an earlier publication arXiv:0712.4404 we find 7 families of massive states of spin 1. Together with the spin 0 states they form 3 families of massive vector multiplets and 2 families of massive gravitino multiplets, containing a vector, a pseudovector and fermions of spin 3/2 and 1/2. In the conformal Klebanov-Witten case these I-odd particles belong to the N=1 superconformal Vector Multiplet I and Gravitino Multiplets II and IV. The operators dual to the I-odd singlet sector include those without bi-fundamental fields making an interesting connection with the pure N=1 SYM theory. We calculate the mass spectrum of the corresponding glueballs numerically and discuss possible applications of our results.

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arXiv2004

Comments on BPS Bound State Decay

In N=2 SYM theory with matter non-conservation of the S-charge of a BPS state under monodromies leads to so-called BPS state "decay". A mechanism for such a behavior on the semiclassical level could be established through consideration of soliton-fermion bound state. Solutions to classical equations of motion allow to observe the BPS state "decay" in vivo.

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