On the influence of the "donor"/"acceptor" presence on the excitation states in molecular chains: non-adiabatic polaron approach

In the paper, we considered a molecular structure that consists of a molecular chain and an additional molecule ("donor"/"acceptor") that can inject (or remove) single excitation (vibron, electron, e.t.c.) onto the molecular chain. We assumed that the excitation forms a self-trapped state due to the interaction with mechanical oscillations of chain structure elements. We analyzed the energy spectra of the excitation and showed that its state (when it migrates to the molecular chain) has the properties of the non-adiabatic polaron state. The conditions under which the excitation can migrate from one subsystem to another were considered. It was shown that the presence of a "donor" molecule cannot significantly change the properties of the excitation located on the molecular chain. At the same time, the molecular chain can affect the position of the energy level of the excitation localized on the "donor" subsystem. Indirectly, this can influence the process of excitation migration from one subsystem to another one. The influence of basic energy parameters of the system and the environment temperature on this process are discussed. The entire system was assumed to be in thermal equilibrium with the environment

Electromagnetic pulse transparency in coupled cavity arrays through dispersion management

We theoretically demonstrated the possible emergence of slow-light self-induced transparency solitons in the infinite one-dimensional coupled cavity array, with each cavity containing a single qubit. We have predicted a substantial dependence of pulse transparency on its dimensionless width $\tau_0$. In particular, short pulses whose widths range from $\tau_0\ll 1$ to $\tau_0\lesssim 1$ exhibit simple, almost linear dispersion law with a finite frequency gap of the order of the cavity array photonic band gap. That is, the medium is opaque for very short pulses with carrier wave frequency below the photonic gap. When the pulse width exceeds the critical one, a twin transparency window separated by a finite band gap appears in the soliton pulse dispersion law. Observation of predicted effects within the proposed setup would be of interest for understanding the properties of self-induced transparency effect in general and future applications in the design of quantum technological devices

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

Biomolecular pathways are built from diverse types of pairwise interactions, ranging from physical protein-protein interactions and modifications to indirect regulatory relationships. One goal of systems biology is to bridge three aspects of this complexity: the growing body of high-throughput data assaying these interactions; the specific interactions in which individual genes participate; and the genome-wide patterns of interactions in a system of interest. Here, we describe methodology for simultaneously predicting specific types of biomolecular interactions using high-throughput genomic data. This results in a comprehensive compendium of whole-genome networks for yeast, derived from ∼3,500 experimental conditions and describing 30 interaction types, which range from general (e.g. physical or regulatory) to specific (e.g. phosphorylation or transcriptional regulation). We used these networks to investigate molecular pathways in carbon metabolism and cellular transport, proposing a novel connection between glycogen breakdown and glucose utilization supported by recent publications. Additionally, 14 specific predicted interactions in DNA topological change and protein biosynthesis were experimentally validated. We analyzed the systems-level network features within all interactomes, verifying the presence of small-world properties and enrichment for recurring network motifs. This compendium of physical, synthetic, regulatory, and functional interaction networks has been made publicly available through an interactive web interface for investigators to utilize in future research at http://function.princeton.edu/bioweaver/

Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases

Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult. We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell. For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases. The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download

Qubit-Photon Bound States in Superconducting Metamaterials

We study quantum features of electromagnetic radiation propagating in the one-dimensional superconducting quantum metamaterial comprised of an infinite chain of charge qubits placed within two-stripe massive superconductive resonators. The Quantum-mechanical model is derived assuming weak fields and that, at low temperatures, each qubit is either unoccupied ($N=0$) or occupied by a single Cooper pair ($N=1$). Based on this assumption we demonstrate the emergence of two bands of single-photon-qubit bound states with the energy lying within (lower branch) or outside (higher) the photon continuum. The emergence of bound states may cause radiation trapping which could be of interest for the control of photon transport in these systems

Relationships between nitrogen utilization and grain technological quality in durum wheat: I. Nitrogen translocation and nitrogen use efficiency for protein.

Durum wheat (Triticum durum Desf.) is widely cultivated in the Mediterranean area where plants generally suffer from water stress during grain-filling period. This study was conducted to evaluate the influence of N levels and water regimes on N translocation and nitrogen use efficiency for protein (NUEP) in durum wheat grown under Mediterranean conditions. A 2-yr experiment was performed in southern Italy using four cultivars, two water regimes (irrigated and rainfed) and three N levels (0, 60, and 120 kg ha–1). Among the cultivars under study, Simeto showed the highest N translocation in both years and, together with Ofanto, also the highest NUEP values, especially in rainfed condition. This highlights their good adaptability to dry Southern Italy environment. Nitrogen fertilization caused a general decrease of NUEP and its components in both growing seasons; this was more evident in the first drier year, mainly due to a decrease in N uptake. Under water stress the higher N level caused a decrease in N translocation, N translocation efficiency, and grain N content. The contribution of translocated N to grain N content was 75% in the wetter year and 57% in the drier year, showing that in drought condition preanthesis N assimilation was lower. In conclusion under water stress condition the higher N level (120 kg ha–1), despite determining an increase in plant N content, did not imply an increase in grain N content, due to a decrease in N translocation and efficiency