Conformal Regime Research Articles

Complete Diagram of Conformational Regimes for Polyampholytic Disordered Proteins

Complete Diagram of Conformational Regimes for Polyampholytic Disordered Proteins

Transient Relativistic Fluid Dynamics in a General Hydrodynamic Frame.

We propose a new theory of second-order viscous relativistic hydrodynamics which does not impose any frame conditions on the choice of the hydrodynamic variables. It differs from Mueller-Israel-Stewart theory by including additional transient degrees of freedom, and its first-order truncation reduces to Bemfica-Disconzi-Noronha-Kovtun theory. Conditions for causality and stability are explicitly given in the conformal regime. As an illustrative example, we consider Bjorken flow solutions to our equations and identify variables which make a hydrodynamic attractor manifest.

Thermalization of holographic excited states

We propose a real time holographic framework to study thermalization processes of a family of QFT excited states. The construction builds on Skenderis-van Rees’s holographic duals to QFT Schwinger-Keldysh complex-time ordered paths. Thermalization is explored choosing a set of observables Fn which essentially isolate the excited state contribution. Focusing on theories defined on compact manifolds and with excited states defined in terms of Euclidean path integrals, we identify boundary conditions that allow to avoid any number of modes in the initial field state. In the large conformal dimensions regime, we give precise prescriptions on how to compute the observables in terms of bulk geodesics.

Synthesis of core-brush fluorescent silica nanoparticles with tunable hydrophilicity by ATRP method

Polymer coating on fluorescent silica nanoparticles enables to tailor made nanocomposite with unique tunable properties. Combining the emission of a fluorescent probe and the surface chemistry of a polymer shell a wide range of applications can be cover. The changing in the conformation of polymer chains enables to modify the hydrophilicity of the functionalized particles. For this, zwitterionic polymers are optimal since the electrostatic interaction between charged groups determines the conformational regime of the chains and the colloidal stability of the particle. In this work, we propose a functionalization of Amino Fluorescent Silica Nanoparticles (Amino-NPF) with a zwitterionic polymer by ATRP method. Poly [2- (Methacryloyloxy) ethyl] dimethyl- (3-sulfopropyl) ammonium hydroxide (PDMAPS) was successfully grafted onto the Amino-NPF surface. In particular, we followed three routes with different amount of catalyst. Route 1 corresponds to non-Cu (II) in solution, while pathways 2 and 3 consist of an increment in the metal concentration, 10% and 60% relative to Cu (I), respectively. A very short reaction time, only 15 min, was employed to diminish or avoid radical-radical termination. The stability and dispersability of the obtained core-brush nanoparticles in different solvents was evaluated. We demonstrate that the Cu (II) to Cu (I) concentration ratio defines the conformation of the polymer chains and in turn the hydrophilic character of the particles.

The quantum p-spin glass model: a user manual for holographers

We study a large-N bosonic quantum mechanical sigma-model with a spherical target space subject to disordered interactions, more colloquially known as the p-spin spherical model. Replica symmetry is broken at low temperatures and for sufficiently weak quantum fluctuations, which drives the system into a spin glass (SG) phase. The first half of this paper is dedicated to a discussion of this model’s thermodynamics, with particular emphasis on the marginally stable SG. This phase exhibits an emergent conformal symmetry in the strong coupling regime, which dictates its thermodynamic properties. It is associated with an extensive number of nearby states in the free energy landscape. We discuss in detail an elegant approximate solution to the SG equations, which interpolates between the conformal regime and an ultraviolet-complete short distance solution. In the second half of this paper we explore the real-time dynamics of the model and uncover quantum chaos as measured by out-of-time-order four-point functions, both numerically and analytically. We find exponential Lyapunov growth, which intricately depends on the model’s couplings and becomes strongest in the quantum critical regime. We emphasize that the SG phase also exhibits quantum chaos, albeit with parametrically smaller Lyapunov exponent than in the replica symmetric phase. An analytical calculation in the marginal SG phase suggests that this Lyapunov exponent vanishes in a particular infinite coupling limit. We comment on the potential meaning of these observations from the perspective of holography.

Mass Spectra in $$\boldsymbol{\mathcal{N}=1SQCD}$$ with Additional Colorless Fields and Problems with the Seiberg Duality

Considered is the direct ${\cal N}=1$ SQCD-like $\Phi$-theory with $SU(N_c)$ colors and $3N_c/2< N_F<2N_c$ flavors of light quarks ${\overline Q},\,Q$. Besides, it includes $N^2_F$ additional colorless but flavored fields $\Phi_{i}^{j}$ with the large mass parameter $\mu_{\Phi}\gg\Lambda_Q$, interacting with quarks through the Yukawa coupling. In parallel, is considered its Seiberg's dual variant, i.e. the $d\Phi$-theory with $(N_F-N_c)$ dual colors, $N_F$ flavors of dual quarks ${\overline q},\,{q}$ and $N_F^2$ elementary mion fields $M^i_j\rightarrow ({\overline Q}_j Q^i)$. In considered here vacua, the quarks of both theories are in the conformal regimes at scales $\mu<\Lambda_Q$. The mass spectra are calculated in sections 4 and 5. It is shown that they are different in the direct and dual theories, in disagreement with the Seiberg hypothesis about equivalence of two such theories. Besides it is shown in the direct theory that a qualitatively new phenomenon takes place: the seemingly heavy fields $\Phi$ `return back' and there appear two additional generations of light $\Phi$-particles with small masses $\mu^{\rm pole}_{2,3}(\Phi)\ll\Lambda_Q$. In Conclusions also presented comparison of mass spectra of these two theories for such values of parameters when the direct theory is in the very strong coupling regime, while the dual one is in the weak coupling IR-free logarithmic regime. It is shown that mass spectra of these two theories are parametrically different in this case.

Feynman diagrams and the large charge expansion in 3 − ε dimensions

In arXiv:1909.01269 it was shown that the scaling dimension of the lightest charge n operator in the U(1) model at the Wilson-Fisher fixed point in D=4−ε can be computed semiclassically for arbitrary values of λn, where λ is the perturbatively small fixed point coupling. Here we generalize this result to the fixed point of the U(1) model in 3−ε dimensions. The result interpolates continuously between diagrammatic calculations and the universal conformal superfluid regime for CFTs at large charge. In particular it reproduces the expectedly universal O(n0) contribution to the scaling dimension of large charge operators in 3D CFTs.

On quantum quenches at one loop

We study global quenches in a number of interacting quantum field theory models away from the conformal regime. We conduct a perturbative renormalization at one-loop level and track the modifications of the quench protocol induced by the renormalization group flow. The scaling of various observables at early times is evaluated in the regime of rapid quench rates, with a particular emphasis placed on the leading order effects that cannot be recovered using the finite order conformal perturbation theory. We employ the canonical ideas of effective action to verify our results and discuss a potential route towards understanding the late time dynamics.

The bar-hinge motor: a synthetic protein design exploiting conformational switching to achieve directional motility

One challenge to synthetic biology is to design functional machines from natural building blocks, from individual amino acids up to larger motifs such as the coiled coil. Here we investigate a novel bipedal motor concept, the Bar-Hinge Motor (BHM), a peptide-based motor capable of executing directed motion via externally controlled conformational switching between a straight bar and a V-shaped hinged form. Incorporating ligand-regulated binding to a DNA track and periodic control of ligand supply makes the BHM an example of a ‘clocked walker’. Here, we employ a coarse-grained computational model for the BHM to assess the feasibility of a proposed experimental realization, with conformational switching regulated through the photoisomerization of peptide-bound azobenzene molecules. The results of numerical simulations using the model show that the incorporation of this conformational switch is necessary for the BHM to execute directional, rather than random, motion on a one-dimensional track. The power-stroke-driven directed motion is seen in the model even under conditions that underestimate the level of control we expect to be able to produce in the experimental realisation, demonstrating that this type of design should be an excellent vehicle for exploring the physics behind protein motion. By investigating its force-dependent dynamics, we show that the BHM is capable of directional motion against an applied load, even in the more relaxed conformational switching regimes. Thus, BHM appears to be an excellent candidate for a motor design incorporating a power stroke, enabling us to explore the ability of switchable coiled-coil designs to deliver power strokes within synthetic biology.

Holographic gauged NJL model: The conformal window and ideal walking

We study the holographic Dynamic AdS/QCD description of a SU($N_c$) non-abelian gauge theory with $N_f$ fermions in the fundamental representation which also have Nambu-Jona-Lasinio interactions included using Witten's multi-trace prescription. In particular here we study aspects of the dynamics in and near the conformal window of the gauge theory as described by the two loop running of the gauge theory. If the number of flavours is such that the IR fixed point lies with the anomalous dimension, $\gamma$, of the quark bilinear above one then chiral symmetry breaking occurs. Here we display a spiral in the mass - quark condensate plane describing a sequence of unstable excited states of the vacuum. An attractive NJL operator enhances the vacuum condensate but only an infinitely repulsive NJL interaction switches off the condensation completely. When $N_f$ changes so that the IR fixed point falls below one (the conformal window region) there is a numerical discontinuity in the phase structure with condensation only occurring with a super critical NJL interaction. In the conformal window, the running of $\gamma$ to a non-trivial IR fixed point is similar to walking dynamics, although chiral symmetry breaking is not triggered. In the "Ideal Walking" scenario, chiral symmetry is broken in that IR conformal regime by the NJL interaction, but the change in $\gamma$ enhances the UV condensate. That enhancement of the condensate is shown in an analytic model with a sharp change in $\gamma$ and we show equivalent numerical results for the case of the two loop running. In the model the $\sigma$ becomes massless as the gauge theory running becomes near conformal and we show it is possible to realize a light higgs-like state in Ideal Walking models.

Low-high voltage duality in tunneling spectroscopy of the Sachdev-Ye-Kitaev model

The Sachdev-Ye-Kitaev (SYK) model describes a strongly correlated metal with all-to-all random interactions (average strength $J$) between $N$ fermions (complex Dirac fermions or real Majorana fermions). In the large-$N$ limit a conformal symmetry emerges that renders the model exactly soluble. Here we study how the non-Fermi liquid behavior of the closed system in equilibrium manifests itself in an open system out of equilibrium. We calculate the current-voltage characteristic of a quantum dot, described by the complex-valued SYK model, coupled to a voltage source via a single-channel metallic lead (coupling strength $\Gamma$). A one-parameter scaling law appears in the large-$N$ conformal regime, where the differential conductance $G=dI/dV$ depends on the applied voltage only through the dimensionless combination $\xi=eVJ/\Gamma^2$. Low and high voltages are related by the duality $G(\xi)=G(\pi/\xi)$. This provides for an unambiguous signature of the conformal symmetry in tunneling spectroscopy.

Morphological stabilization and KPZ scaling by electrochemically induced co-deposition of nanostructured NiW alloy films

We have assessed the stabilizing role that induced co-deposition has in the growth of nanostructured NiW alloy films by electrodeposition on polished steel substrates, under pulsed galvanostatic conditions. We have compared the kinetic roughening properties of NiW films with those of Ni films deposited under the same conditions, as assessed by Atomic Force Microscopy. The surface morphologies of both systems are super-rough at short times, but differ at long times: while a cauliflower-like structure dominates for Ni, the surfaces of NiW films display a nodular morphology consistent with more stable, conformal growth, whose height fluctuations are in the Kardar-Parisi-Zhang universality class of rough two-dimensional interfaces. These differences are explained by the mechanisms controlling surface growth in each case: mass transport through the electrolyte (Ni) and attachment of the incoming species to the growing interface (NiW). Thus, the long-time conformal growth regime is characteristic of electrochemical induced co-deposition under current conditions in which surface kinetics is hindered due to a complex reaction mechanism. These results agree with a theoretical model of surface growth in diffusion-limited systems, in which the key parameter is the relative importance of mass transport with respect to the kinetics of the attachment reaction.

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains.

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor-acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent with a globule-like conformation in a poor solvent. Overall, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.

Parotid gland mean dose as a xerostomia predictor in low-dose domains

Purpose: Xerostomia is a common side effect of radiotherapy resulting from excessive irradiation of salivary glands. Typically, xerostomia is modeled by the mean dose-response characteristic of parotid glands and prevented by mean dose constraints to either contralateral or both parotid glands. The aim of this study was to investigate whether normal tissue complication probability (NTCP) models based on the mean radiation dose to parotid glands are suitable for the prediction of xerostomia in a highly conformal low-dose regime of modern intensity-modulated radiotherapy (IMRT) techniques.Material and methods: We present a retrospective analysis of 153 head and neck cancer patients treated with radiotherapy. The Lyman Kutcher Burman (LKB) model was used to evaluate predictive power of the parotid gland mean dose with respect to xerostomia at 6 and 12 months after the treatment. The predictive performance of the model was evaluated by receiver operating characteristic (ROC) curves and precision-recall (PR) curves.Results: Average mean doses to ipsilateral and contralateral parotid glands were 25.4 Gy and 18.7 Gy, respectively. QUANTEC constraints were met in 74% of patients. Mild to severe (G1+) xerostomia prevalence at both 6 and 12 months was 67%. Moderate to severe (G2+) xerostomia prevalence at 6 and 12 months was 20% and 15%, respectively. G1 + xerostomia was predicted reasonably well with area under the ROC curve ranging from 0.69 to 0.76. The LKB model failed to provide reliable G2 + xerostomia predictions at both time points.Conclusions: Reduction of the mean dose to parotid glands below QUANTEC guidelines resulted in low G2 + xerostomia rates. In this dose domain, the mean dose models predicted G1 + xerostomia fairly well, however, failed to recognize patients at risk of G2 + xerostomia. There is a need for the development of more flexible models able to capture complexity of dose response in this dose regime.

Compactness results for static and dynamic chiral skyrmions near the conformal limit

We examine lower order perturbations of the harmonic map problem from $$\mathbb {R}^2$$ to $$\mathbb {S}^2$$ including chiral interaction in form of a helicity term that prefers modulation, and a potential term that enables decay to a uniform background state. Energy functionals of this type arise in the context of magnetic systems without inversion symmetry. In the almost conformal regime, where these perturbations are weighted with a small parameter, we examine the existence of relative minimizers in a non-trivial homotopy class, so-called chiral skyrmions, strong compactness of almost minimizers, and their asymptotic limit. Finally we examine dynamic stability and compactness of almost minimizers in the context of the Landau–Lifshitz–Gilbert equation including spin-transfer torques arising from the interaction with an external current.

Solvable model for a dynamical quantum phase transition from fast to slow scrambling

We propose an extension of the Sachdev-Ye-Kitaev (SYK) model that exhibits a quantum phase transition from the previously identified non-Fermi liquid fixed point to a Fermi liquid like state, while still allowing an exact solution in a suitable large $N$ limit. The extended model involves coupling the interacting $N$-site SYK model to a new set of $pN$ peripheral sites with only quadratic hopping terms between them. The conformal fixed point of the SYK model remains a stable low energy phase below a critical ratio of peripheral sites $p<p_c(n)$ that depends on the fermion filling $n$. The scrambling dynamics throughout the non-Fermi liquid phase is characterized by a universal Lyapunov exponent $\lambda_L\to 2\pi T$ in the low temperature limit, however the temperature scale marking the crossover to the conformal regime vanishes continuously at the critical point $p_c$. The residual entropy at $T\to 0$, non zero in the NFL, also vanishes continuously at the critical point. For $p>p_c$ the quadratic sites effectively screen the SYK dynamics, leading to a quadratic fixed point in the low temperature and frequency limit. The interactions have a perturbative effect in this regime leading to scrambling with Lyapunov exponent $\lambda_L\propto T^2$.

Impact of surface grafting density of PEG macromolecules on dually fluorescent silica nanoparticles used for the in vivo imaging of subcutaneous tumors.

In the context of systematically administered nanomedicines, the physicochemistry of NP surfaces must be controlled as a prerequisite to improve blood circulation time, and passive and active targeting. In particular, there is a real need to develop NP stealth and labelling for both in vivo and microscopic fluorescence imaging in a mice model. We have synthesized NIR/red dually fluorescent silica nanoparticles of 19nm covalently covered by a PEG layer of different grafting density in the brush conformational regime by using a reductive amination reaction. These particles were characterized by TEM, DRIFT, DLS, TGA, ζ potential measurements, UV-vis and fluorescence spectroscopy. Prostate tumors were generated in mice by subcutaneous injection of RM1-CMV-Fluc cells. Tumor growth was monitored by BLI after a D-luciferin injection. Four samples of PEGylated fluorescent NPs were individually intravenously injected into 6 mice (N=6, total 24 mice). Nanoparticle distribution was investigated using in vivo fluorescence reflectance imaging (FRI) over 48h and microscopy imaging was employed to localize the NPs within tumors in vitro. Fluorescent NP accumulation, due to the enhanced permeability and retention (EPR) effect, increases gradually as a function of increased PEG surface grafting density with a huge difference observed for the highest density grafting. For the highest grafting density, a blood circulation time of up to 24h was observed with a strong reduction in uptake by the liver. In vivo experimental results suggest that the biodistribution of NPs is very sensitive to slight variations in surface grafting density when the NPs present a high curvature radius. This study underlines the need to compensate a high curvature radius with a PEG-saturated NP surface to improve blood circulation and accumulation within tumors through the EPR effect. Dually fluorescent NPs PEGylated to saturation display physical properties useful for assessing the susceptibility of tumors to the EPR effect. Control of the physicochemical features of nanoparticle surfaces to improve blood circulation times and monitoring of the EPR effect. This article is part of a Special Issue entitled "Recent Advances in Bionanomaterials" Guest Editor: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

Topological constraints, such as those associated with DNA supercoiling, play an integral role in genomic regulation and organization in living systems. However, physical understanding of the principles that underlie DNA organization at biologically relevant length scales remains a formidable challenge. We develop a coarse-grained simulation approach for predicting equilibrium conformations of supercoiled DNA. Our methodology enables the study of supercoiled DNA molecules at greater length scales and supercoiling densities than previously explored by simulation. With this approach, we study the conformational transitions that arise due to supercoiling across the full range of supercoiling densities that are commonly explored by living systems. Simulations of ring DNA molecules with lengths at the scale of topological domains in the Escherichia coli chromosome (∼10 kilobases) reveal large-scale conformational transitions elicited by supercoiling. The conformational transitions result in three supercoiling conformational regimes that are governed by a competition among chiral coils, extended plectonemes, and branched hyper-supercoils. These results capture the nonmonotonic relationship of size versus degree of supercoiling observed in experimental sedimentation studies of supercoiled DNA, and our results provide a physical explanation of the conformational transitions underlying this behavior. The length scales and supercoiling regimes investigated here coincide with those relevant to transcription-coupled remodeling of supercoiled topological domains, and we discuss possible implications of these findings in terms of the interplay between transcription and topology in bacterial chromosome organization.

Large mass hierarchies from strongly-coupled dynamics

Besides the Higgs particle discovered in 2012, with mass 125 GeV, recent LHC data show tentative signals for new resonances in diboson as well as diphoton searches at high center-of-mass energies (2 TeV and 750 GeV, respectively). If these signals are confirmed (or other new resonances are discovered at the TeV scale), the large hierarchies between masses of new bosons require a dynamical explanation. Motivated by these tentative signals of new physics, we investigate the theoretical possibility that large hierarchies in the masses of glueballs could arise dynamically in new strongly-coupled gauge theories extending the standard model of particle physics. We study lattice data on non-Abelian gauge theories in the (near-)conformal regime as well as a simple toy model in the context of gauge/gravity dualities. We focus our attention on the ratio $R$ between the mass of the lightest spin-2 and spin-0 resonances, that for technical reasons is a particularly convenient and clean observable to study. For models in which (non-perturbative) large anomalous dimensions arise dynamically, we show indications that this mass ratio can be large, with $R>5$. Moreover, our results suggest that $R$ might be related to universal properties of the IR fixed point. Our findings provide an interesting step towards understanding large mass ratios in the non-perturbative regime of quantum field theories with (near) IR conformal behaviour.

The blow-up rate for strongly perturbed semilinear wave equations in the conformal regime without a radial assumption

We consider in this paper a large class of perturbed semilinear wave equations with critical (in the conformal trans- form sense) power nonlinearity. We will show that the blow-up rate of any singular solution is given by the solution of the non-perturbed associated ODE. The result in the radial case has been proved in Math. Phys. Anal. Geom. 18(1) (2015), Art. 15. The same approach will be followed here, but the main difference is to construct a Lyapunov functional in similarity variables valid in the non-radial case, which is far from being trivial. That functional is obtained by combining some classical estimates and a new identity of the Pohozaev type obtained by multiplying Eq. (1.7) by y ·∇ w in a suitable weighted space.