Numerical study of the optical nonlinearity of doped and gapped graphene: From weak to strong field excitation

Numerically solving the semiconductor Bloch equations within a phenomenological relaxation time approximation, we extract both the linear and nonlinear optical conductivities of doped graphene and gapped graphene under excitation by a laser pulse. We discuss in detail the dependence of second harmonic generation, third harmonic generation, and the Kerr effects on the doping level, the gap, and the electric field amplitude. The numerical results for weak electric fields agree with those calculated from available analytic perturbation formulas. For strong electric fields when saturation effects are important, all the effective third order nonlinear response coefficients show a strong field dependence.Comment: 12 pages with 9 figure

Third order nonlinearity of graphene: effects of phenomenological relaxation and finite temperature

We investigate the effect of phenomenological relaxation parameters on the third order optical nonlinearity of doped graphene by perturbatively solving the semiconductor Bloch equation around the Dirac points. An analytic expression for the nonlinear conductivity at zero temperature is obtained under the linear dispersion approximation. With this analytic formula as starting point, we construct the conductivity at finite temperature and study the optical response to a laser pulse of finite duration. We illustrate the dependence of several nonlinear optical effects, such as third harmonic generation, Kerr effects and two photon absorption, parametric frequency conversion, and two color coherent current injection, on the relaxation parameters, temperature, and pulse duration. In the special case where one of the electric fields is taken as a dc field, we investigate the dc-current and dc-field induced second order nonlinearities, including dc-current induced second harmonic generation and difference frequency generation.Comment: 23+ pages, 10 figures. In this version we correct a sign typo in Eq. (25), for which we thank the discussion in the work http://arxiv.org/abs/1506.00534v

Dynamic response of structural elements exposed to sonic booms

Dynamic response of uniform beams and plates exposed to sonic boom

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