Anomalies of ac driven solitary waves with internal modes: Nonparametric resonances induced by parametric forces

We study the dynamics of kinks in the $\phi^4$ model subjected to a parametric ac force, both with and without damping, as a paradigm of solitary waves with internal modes. By using a collective coordinate approach, we find that the parametric force has a non-parametric effect on the kink motion. Specifically, we find that the internal mode leads to a resonance for frequencies of the parametric driving close to its own frequency, in which case the energy of the system grows as well as the width of the kink. These predictions of the collective coordinate theory are verified by numerical simulations of the full partial differential equation. We finally compare this kind of resonance with that obtained for non-parametric ac forces and conclude that the effect of ac drivings on solitary waves with internal modes is exactly the opposite of their character in the partial differential equation.Comment: To appear in Phys Rev

Internal mode mechanism for collective energy transport in extended systems

We study directed energy transport in homogeneous nonlinear extended systems in the presence of homogeneous ac forces and dissipation. We show that the mechanism responsible for unidirectional motion of topological excitations is the coupling of their internal and translation degrees of freedom. Our results lead to a selection rule for the existence of such motion based on resonances that explains earlier symmetry analysis of this phenomenon. The direction of motion is found to depend both on the initial and the relative phases of the two harmonic drivings, even in the presence of noise.Comment: Final version, to appear in Physical Review Letter

Anomalous resonance phenomena of solitary waves with internal modes

We investigate the non-parametric, pure ac driven dynamics of nonlinear Klein-Gordon solitary waves having an internal mode of frequency $\Omega_i$. We show that the strongest resonance arises when the driving frequency $\delta=\Omega_i/2$, whereas when $\delta=\Omega_i$ the resonance is weaker, disappearing for nonzero damping. At resonance, the dynamics of the kink center of mass becomes chaotic. As we identify the resonance mechanism as an {\em indirect} coupling to the internal mode due to its symmetry, we expect similar results for other systems.Comment: 4 pages, 4 figures, to appear in Phys Rev Let

On the existence of internal modes of sine-Gordon kinks

We study whether or not sine-Gordon kinks exhibit internal modes or ``quasimodes.'' By considering the response of the kinks to ac forces and initial distortions, we show that neither intrinsic internal modes nor ``quasimodes'' exist in contrast to previous reports. However, we do identify a different kind of internal mode bifurcating from the bottom edge of the phonon band which arises from the discretization of the system in the numerical simulations, thus confirming recent predictions.Comment: 4 pages, 2 figures, REVTeX, to appear as a Rapid Communication in Phys Rev E (July 1st

Overdamped sine-Gordon kink in a thermal bath

We study the sine-Gordon kink diffusion at finite temperature in the overdamped limit. By means of a general perturbative approach, we calculate the first- and second-order (in temperature) contributions to the diffusion coefficient. We compare our analytical predictions with numerical simulations. The good agreement allows us to conclude that, up to temperatures where kink-antikink nucleation processes cannot be neglected, a diffusion constant linear and quadratic in temperature gives a very accurate description of the diffusive motion of the kink. The quadratic temperature dependence is shown to stem from the interaction with the phonons. In addition, we calculate and compute the average value $$ of the wave function as a function of time and show that its width grows with $\sqrt{t}$. We discuss the interpretation of this finding and show that it arises from the dispersion of the kink center positions of individual realizations which all keep their width.Comment: REVTeX, 12 pages, 10 figures, to appear in Phys Rev

Resonances in the dynamics of ϕ4\phi^4 kinks perturbed by ac forces

We study the dynamics of $\phi^4$ kinks perturbed by an ac force, both with and without damping. We address this issue by using a collective coordinate theory, which allows us to reduce the problem to the dynamics of the kink center and width. We carry out a careful analysis of the corresponding ordinary differential equations, of Mathieu type in the undamped case, finding and characterizing the resonant frequencies and the regions of existence of resonant solutions. We verify the accuracy of our predictions by numerical simulation of the full partial differential equation, showing that the collective coordinate prediction is very accurate. Numerical simulations for the damped case establish that the strongest resonance is the one at half the frequency of the internal mode of the kink. In the conclusion we discuss on the possible relevance of our results for other systems, especially the sine-Gordon equation. We also obtain additional results regarding the equivalence between different collective coordinate methods applied to this problem.Comment: 23 pages, 7 figures, REVTeX, accepted for publication in Phys. Rev.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment