Search results for "Quantitative Biology::Genomics"
showing 10 items of 39 documents
Tunable arrayed waveguide grating driven by surface acoustic waves
2016
We present a design approach for compact reconfigurable phased-array wavelength-division multiplexing (WDM) devices with N access waveguides (WGs) based on multimode interference (MMI) couplers. The proposed devices comprise two MMI couplers which are employed as power splitters and combiners, respectively, linked by an array of N single-mode WGs. First, passive devices are explored. Taking advantage of the transfer phases between the access ports of the MMI couplers, we derive very simple phase relations between the arms that provide wavelength dispersion at the output plane of the devices. When the effective refractive index of the WGs is modulated with the proper relative optical phase d…
Influence of structure on the polarizability of hydrated methane sulfonic acid clusters
2015
Abstract: The relationship between polarizability and structure is investigated in methane sulfonic acid (MSA) and in 36 hydrated MSA clusters. The polarizabilities are calculated at B3LYP and MP2 level and further partitioned into molecular contributions using classic and iterative Hirshfeld methods. The differences in the two approaches for partitioning of polarizabilities are thoroughly analyzed. The polarizabilities of the molecules are found to be influenced in a systematic way by the hydrogen bond network in the clusters, proton transfer between MSA and water molecules, and weak interactions between water molecules and the methyl group of MSA.
Banach spaces which are r-uniformly noncreasy
2003
Abstract We consider a family of spaces wider than UNC spaces introduced by Prus, and we give some fixed point results in the setting of these spaces.
A characterization of regular circular languages generated by marked splicing systems
2009
AbstractSplicing systems are generative devices of formal languages, introduced by Head in 1987 to model biological phenomena on linear and circular DNA molecules. A splicing system is defined by giving an initial set I and a set R of rules. Some unanswered questions are related to the computational power of circular splicing systems. In particular, a still open question is to find a characterization of circular languages generated by finite circular splicing systems (i.e., circular splicing systems with both I and R finite sets). In this paper we introduce a special class of the latter systems named marked systems. We prove that a marked system S generates a regular circular language if an…
Three new physics realizations of the genetic code and the role of dark matter in bio-systems
2010
TGD inspired quantum biology leads naturally to the idea that several realizations of genetic code exist. Besides the realizations based on temporal patterns of electromagnetic �elds I have considered three di�erent new physics realizations of the genetic code based the notions of many- sheeted space-time, magnetic body, and the hierarchy of Planck constants explaining dark matter in TGD framework. 1. The �rst realization - proposed in the model for DNA as topological quantum computer (tqc) - maps the nucleotides A,G and T,C to dark quarks u,d and their anti-quarks assignable to the ends of magnetic ux tubes representing braid strands and connecting nucleotides to lipids of cell membrane. 2…
Single-molecule FRET studies of counterion effects on the free energy landscape of human mitochondrial lysine tRNA.
2011
The folding energy landscape of RNA is greatly affected by interactions between the RNA and counterions that neutralize the backbone negative charges and may also participate in tertiary contacts. Valence, size, coordination number, and electron shell structure can all contribute to the energetic stabilization of specific RNA conformations. Using single-molecule fluorescence resonance energy transfer (smFRET), we have examined the folding properties of the RNA transcript of human mitochondrial tRNA(Lys), which possesses two different folded states in addition to the unfolded one under conditions of thermodynamic equilibrium. We have quantitatively analyzed the degree of RNA tertiary structu…
The Notion of Wave Genome and DNA as Topological Quantum Computer
2010
Peter Gariaev and collaborators have reported several strange effects of laser light and also ordinary light on DNA. These findings include the rotation of polarization plane of laser light by DNA, phantom DNA effect, the transformation of laser light to radio-wave photons having biological effects, the coding of DNA sequences to the modulated polarization plane of laser light and the ability of this kind of light to induce gene expression in another organisms provided the modulated polarization pattern corresponds to an "address" characterizing the organism, and the formation of images of what is believed to be DNA sample itself and of the objects of environment by DNA sample in a cell irr…
Singlet-Triplet States Interaction Regions in DNA/RNA Nucleobase Hypersurfaces.
2010
The present study provides new insight into the intrinsic mechanisms for the population of the triplet manifold in DNA nucleobases by determining, at the multiconfigurational CASSCF/CASPT2 level, the singlet-triplet states crossing regions and the main decay paths for their lowest singlet and triplet states after near-UV irradiation. The studied singlet-triplet interacting regions are accessible along the minimum energy path of the initially populated singlet bright (1)ππ* state. In particular, all five natural DNA/RNA nucleobases have, at the end of the main minimum energy path and near a conical intersection of the ground and (1)ππ* states, a low-energy, easily accessible, singlet-triplet…
Photostability and Photoreactivity in Biomolecules: Quantum Chemistry of Nucleic Acid Base Monomers and Dimers
2008
The great potentials of high-level ab initio methods, in particular, the CASPT2//CASSCF protocol, are fully illustrated through: (i) the study of ultrafast energy relaxation in DNA/RNA base monomers, (ii) the intrinsic population mechanism of the lowest triplet state, and (iii) how bioexcimers can be considered as precursors of charge transfer and photoinduced reactivity. In order to describe these processes properly, the presence of conical intersections (CIs) and the topology of the involved pathways have to be determined correctly. Thus, in theoretical calculations the dynamic electronic correlation has to be considered. The accessibility of the CIs (or the seam of CIs) becomes crucial t…
Appendix D. Pairwise Pearson correlation coefficients between the commercial and ecological traits considered in the meta-analysis.
2016
Pairwise Pearson correlation coefficients between the commercial and ecological traits considered in the meta-analysis.