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The Dicke model is a staple of theoretical cavity Quantum Electrodynamics (cavity QED), describing the interaction between an ensemble of atoms and a single radiation mode of an optical cavity. It has been studied both quantum mechanically…
Gene regulation in higher eukaryotes involves a complex interplay between the gene proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive spatio-temporal expression. The experimental…
A new deep neural network based on the WaveNet architecture (WNN) is presented, which is designed to grasp specific patterns in the NMR spectra. When trained at a fixed non-uniform sampling (NUS) schedule, the WNN benefits from pattern…
We address a biophysical network dynamical model to study how the modulation of dopamine (DA) activity and related N-methyl-d-aspartate (NMDA) glutamate receptor activity as well as the emerging Pre-Frontal Cortex (PFC) functional…
An existing single resonance model with S11, P11 and P13 Breit-Wiegner resonances in the s-channel has been re-applied to the old pi N --> K Lambda data. It has been shown that the standard set of resonant parameters fails to reproduce the…
Parkinson disease (PD) patients experience pain fluctuations that significantly reduce their quality of life. Despite the vast knowledge of the subthalamic nucleus (STN) role in PD, the STN biomarkers for pain fluctuations and the…
The relationship between sequence variation and phenotype is poorly understood. Here we use metabolomic analysis to elucidate the molecular mechanism underlying the filamentous phenotype of E. coli strains that carry destabilizing mutations…
Dynamic magnetic resonance imaging (DMRI) is an effective imaging tool for diagnosis tasks that require motion tracking of a certain anatomy. To speed up DMRI acquisition, k-space measurements are commonly undersampled along spatial or…
We propose a novel approach based on Denoising Diffusion Probabilistic Models (DDPMs) to control nonlinear dynamical systems. DDPMs are the state-of-art of generative models that have achieved success in a wide variety of sampling tasks. In…
Transcriptional repressor CTCF is an important regulator of chromatin 3D structure, facilitating the formation of topologically associating domains (TADs). However, its direct effects on gene regulation is less well understood. Here, we…
We formulate and analyze a theoretical model for the regulation of microtubule (MT) polymerization dynamics by the signaling proteins Rac1 and stathmin. In cells, the MT growth rate is inhibited by cytosolic stathmin, which, in turn, is…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Medical imaging applications are highly specialized in terms of human anatomy, pathology, and imaging domains. Therefore, annotated training datasets for training deep learning applications in medical imaging not only need to be highly…
Response functions for spin-density-wave (SDW) and d-wave singlet superconductivity ($d$SC) in quasi-one-dimensional (Q1D) electron systems are calculated by a renormalization group technique. It is shown that the response functions for…
The nervous system is today recognized to play an important role in the development of cancer. Indeed, neurons extend long processes (axons) that grow and infiltrate tumors in order to regulate the progression of the disease in a positive…
Transformer is a successful deep neural network (DNN) architecture that has shown its versatility not only in natural language processing but also in music information retrieval (MIR). In this paper, we present a novel Transformer-based…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
We numerically study excitation transfer in an artificial LH1-RC complex -- an $N$-site donor ring coupled to a central acceptor -- driven by a narrowband optical mode and evolved under a Lindblad master equation with loss and dephasing. In…
We have studied effects of perturbations on the cat cerebral cortex. According to the literature, this cortex structure can be described by a clustered network. This way, we construct a clustered network with the same number of areas as in…
Resonant rectifier topologies would be a promising candidate for achieving simple, compact, and reliable single-stage wireless power transfer (WPT) receiver if not for the lack of good DC regulation capability. This paper investigates the…