Riemann–Hilbertov pristup polariziranim solitonima u sredstvu s tri nivoa

Solitons due to the interaction of polarized waves in optically nonlinear media have been analysed using the Riemann-Hilbert transform. We consider the propagation and interaction of differently polarized two-frequency ultrashort optical pulses in a resonant medium consisting of three-level particles. The exact form of the solitons is obtained explicitly.Uporabom Riemann–Hilbertove transformacije proučavaju se solitoni nastali međudjelovanjem polariziranih valova u optički nelinearnom sredstvu. Određena su egzaktna solitonska rješenja za širenje i međudjelovanje dvo–frekventnih ultrakratkih optičkih pulseva različitih polarizacija u rezonantnom sredstvu sa česticama na tri nivoa

Anvelopni solitoni i modulacijska nestabilnost u elektronsko-pozitronskoj plazmi

We have studied the formation of envelope soliton in a electron-positron plasma. The deduced nonlinear Schrödinger equation yields information about the modulational instability of the system for the different ranges of the plasma parameters. It is important to note that the modulational stability depends on the positron-electron density ratio. The theory is applicable to solitary waves in space plasmas.Proučavamo stvaranje anvelopnih solitona u elektronsko-pozitronskoj plazmi. Izvedena nelinearna Schrodingerova jednadžba daje podatke o modulacijskoj nestabilnosti sustava za razna područja parametara plazme. Važno je primijetiti kako modulacijska nestabilnost ovisi o omjeru gustoće elektrona i pozitrona. Teorija se može primijeniti na solitonske valove u svemirskoj plazmi

Anvelopni solitoni i modulacijska nestabilnost u elektronsko-pozitronskoj plazmi

We have studied the formation of envelope soliton in a electron-positron plasma. The deduced nonlinear Schrödinger equation yields information about the modulational instability of the system for the different ranges of the plasma parameters. It is important to note that the modulational stability depends on the positron-electron density ratio. The theory is applicable to solitary waves in space plasmas.Proučavamo stvaranje anvelopnih solitona u elektronsko-pozitronskoj plazmi. Izvedena nelinearna Schrodingerova jednadžba daje podatke o modulacijskoj nestabilnosti sustava za razna područja parametara plazme. Važno je primijetiti kako modulacijska nestabilnost ovisi o omjeru gustoće elektrona i pozitrona. Teorija se može primijeniti na solitonske valove u svemirskoj plazmi

Riemann–Hilbertov pristup polariziranim solitonima u sredstvu s tri nivoa

Solitons due to the interaction of polarized waves in optically nonlinear media have been analysed using the Riemann-Hilbert transform. We consider the propagation and interaction of differently polarized two-frequency ultrashort optical pulses in a resonant medium consisting of three-level particles. The exact form of the solitons is obtained explicitly.Uporabom Riemann–Hilbertove transformacije proučavaju se solitoni nastali međudjelovanjem polariziranih valova u optički nelinearnom sredstvu. Određena su egzaktna solitonska rješenja za širenje i međudjelovanje dvo–frekventnih ultrakratkih optičkih pulseva različitih polarizacija u rezonantnom sredstvu sa česticama na tri nivoa

Modeling Interactions of Flexible Proteins

Proteins are dynamic molecules that mediate most biological processes through interactions with other proteins and biomolecules. A fundamental understanding of the mechanisms governing protein interactions requires intricate knowledge of the three-dimensional structures of biomolecular complexes. Despite advances in experimental structure determination, we have structural insights into only a small fraction of known complexes. Computational modeling provides an invaluable complementary tool to explore protein interactions in a rapid and high-throughput manner. A principal challenge limiting the accuracy of current computational methods is the ability to predict binding-induced conformational changes during protein–protein association. In this dissertation, I address this challenge by creating new tools to predict atomistic models of flexible protein complexes. First, I develop a heterodimer docking protocol that incorporates flexibility by efficiently simulating conformational selection from hundreds of pre-generated backbone conformations and identifies the near-native models with a novel, coarse-grained score function called Motif Dock Score (MDS). On a benchmark of 88 complexes with different degrees of flexibility, this protocol, RosettaDock 4.0, is the first method to successfully dock approximately 50% of complexes with conformational change of up to 2.2 Å. Next, I present the results of our participation in the community-wide blind experiment, Critical Assessment of PRedicted Interactions (CAPRI) rounds 37–45, where I use various docking methods to predict the structures of protein homomer, heteromer and oligosaccharide complexes. In the process, I identify inadequacies in these methods and propose enhancements. Based on the shortcomings identified in CAPRI, I develop a protocol to predict the structure of symmetric homomers from monomeric inputs with a focus on tightly-packed complexes. This method, Rosetta SymDock2, leverages MDS in the coarse-grained phase and simulates subunit flexibility through induced fit by all-atom flexible-backbone refinement. It outperforms competing algorithms by docking 61% of cyclic complexes and 42% of dihedral complexes in a diverse benchmark of 43 homomers. In the course of developing these algorithms, I also discover that the binding energy wells of homomers are narrower, steeper and deeper than those of heterodimers, thus explaining their increased stability. Finally, I present preliminary results to propose data-driven strategies that can overcome current barriers to accurate modeling

Biotransformation of 9-[beta]-d-arabinofurano-syladenine by rat and human erythrocytes

Studies were performed to test whether 9-[beta]--arabinofuranosyladenine (ara-A) would accumulate in erythrocytes as a result of phosphorylation to the nucleotide level. When [3H]ara-A was incubated with whole blood from rat, monkey or man for 2 hr at 37[deg], the drug rapidly equilibrated between erythrocytes and plasma but did not concentrate in the cells. Incubation of [3H]ara-A with rat and human erythrocyte lysates for 2 hr followed by Chromatographie analysis showed that 2-5 per cent of ara-A was converted to nucleotides. In contrast, 10-35 per cent of [14C]adenosine was converted to adenine nucleotides under the same conditions. Incubation of [3H]ara-A with human erythrocyte lysates for 18 hr resulted in a conversion of approx. 40 per cent of the labeled drug to nucleotides. Additional chromatography revealed, however, that the nucleotide fraction contained almost no arabinosyl nucleotides. Rather, 90 per cent of the label in the nucleotide fraction was identified as IMP. These results indicate that only a minor amount, if any, of ara-A was phosphorylated by erythrocyte enzymes to yield arabinosyl nucleotides. An alternative pathway converted much of the labeled drug to ribosyl nucleotides via the deamination of ara-A to ara-hypoxanthine, cleavage to hypoxanthine and conversion of the free hypoxanthine to IMP.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22270/1/0000709.pd

A note on indigenous technical knowledge in Kinnaur and Lahaul-Spiti districts of Himachal Pradesh

Over the years, Indian farmers have leveraged their ancestral know-how and experimented to cultivate different crops in difficult environmental conditions. Of late, however, traditional knowledge and practices have suffered massive erosion, mainly due to the impact of globalization and modernization. In this regard, the objective of the present paper was to document and validate the ITKs in the tribal farming system in Himachal Pradesh. Kinnaur and Lahaul-Spiti districts of Himachal Pradesh were purposively selected for the study owing to their special status of Schedule Tribal Area. Further, three villages from each district were selected randomly covering a sample of 120 farmers. In addition, 5 key informants experienced in particular ITKs were selected from each village for its validation through Quantification of Indigenous Knowledge. The major documented ITKs were classified into appropriate categories such as soil and water management, cropping system, farm implements, post-harvest technology, storage, horticultural crops, food product development, agro-animal based yarns and leaves, medicinal, veterinary science, animal husbandry, and some myths. Further, Kothar, Graat, Suttar, tying of branches of trees, and chicha were revealed as the most useful ITKs in the tribal areas of Kinnaur. In Lahaul-Spiti, Khudh, Sumbhu, Sem, and shaving off of yak’s hair in summer were the most popular ITKs