Understanding Transonic Weapon Bay Flows

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Unveiling the photophysics of thiourea from CASPT2/CASSCF potential energy surfaces and singlet/triplet excited state molecular dynamics simulations

This work describes the decay mechanism of photoexcited thiourea, both in gas phase and in solution, from the information inferred from the topography of the excited and ground state potential energy surfaces and mixed singlet/triplet quantum classical molecular dynamics simulations. Our gas phase results reveal T1/S0 intersystem crossing as the dominant (49%) intrinsic decay channel to the ground state, which reaches a population of 0.28 at the final time of our simulations (10 ps). Population of the T1, would occur after internal conversion to the S1 from the spectroscopic S2 electronic state, followed by S1->T2 intersystem crossing and T2->T1 internal conversion processes. Minor decay channels occurring exclusively along the singlet manifold, i.e. S2->S0 (33%) and S1->S0 (18%), were also observed to play a role in the relaxation of photoexcited thiourea in the gas phase. The explicit incorporation of water-thiourea interactions in our simulations was found to provoke a very significant delay in the decay to the ground state of the system, with no transitions to the S0 being registered during the first 10 ps of our simulations. Intermolecular vibrational energy redistribution and explicit hydrogen bond interaction established between water molecules and the NH2 group of thiourea were found to structurally or energetically hamper the access to the intersystem crossing or internal conversion funnels with the ground state

Reactions at surfaces studied by ab initio dynamics calculations

Due to the development of efficient algorithms and the improvement of computer power it is now possible to map out potential energy surfaces (PES) of reactions at surfaces in great detail. This achievement has been accompanied by an increased effort in the dynamical simulation of processes on surfaces. The paradigm for simple reactions at surfaces -- the dissociation of hydrogen on metal surfaces -- can now be treated fully quantum dynamically in the molecular degrees of freedom from first principles, i.e., without invoking any adjustable parameters. This relatively new field of ab initio dynamics simulations of reactions at surfaces will be reviewed. Mainly the dissociation of hydrogen on clean and adsorbate covered metal surfaces and on semiconductor surfaces will be discussed. In addition, the ab initio molecular dynamics treatment of reactions of hydrogen atoms with hydrogen-passivated semiconductor surfaces and recent achievements in the ab initio description of laser-induced desorption and further developments will be addressed.Comment: 33 pages, 19 figures, submitted to Surf. Sci. Rep. Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Dynamic coordinated control laws in multiple agent models

We present an active control scheme of a kinetic model of swarming. It has been shown previously that the global control scheme for the model, presented in \cite{JK04}, gives rise to spontaneous collective organization of agents into a unified coherent swarm, via a long-range attractive and short-range repulsive potential. We extend these results by presenting control laws whereby a single swarm is broken into independently functioning subswarm clusters. The transition between one coordinated swarm and multiple clustered subswarms is managed simply with a homotopy parameter. Additionally, we present as an alternate formulation, a local control law for the same model, which implements dynamic barrier avoidance behavior, and in which swarm coherence emerges spontaneously.Comment: 20 pages, 6 figure

A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases.

African trypanosomiasis occurs in 36 countries in sub-Saharan Africa with 10,000 reported cases annually. No definitive remedy is currently available and if left untreated, the disease becomes fatal. Structural and biochemical studies of trypanosomal terminal uridylyl transferases (TUTases) demonstrated their functional role in extensive uridylate insertion/deletion of RNA. Trypanosoma brucei RNA Editing TUTase 1 (TbRET1) is involved in guide RNA 3' end uridylation and maturation, while TbRET2 is responsible for U-insertion at RNA editing sites. Two additional TUTases called TbMEAT1 and TbTUT4 have also been reported to share similar function. TbRET1 and TbRET2 are essential enzymes for the parasite viability making them potential drug targets. For this study, we clustered molecular dynamics (MD) trajectories of four TUTases based on active site shape measured by Pocket Volume Measurer (POVME) program. Among the four TUTases, TbRET1 exhibited the largest average pocket volume, while TbMEAT1's and TbTUT4's active sites displayed the most flexibility. A side pocket was also identified within the active site in all TUTases with TbRET1 having the most pronounced. Our results indicate that TbRET1's larger side pocket can be exploited to achieve selective inhibitor design as FTMap identifies it as a druggable pocket