Shapes and Dynamics from the Time-Dependent Mean Field

Explaining observed properties in terms of underlying shape degrees of freedom is a well--established prism with which to understand atomic nuclei. Self--consistent mean--field models provide one tool to understand nuclear shapes, and their link to other nuclear properties and observables. We present examples of how the time--dependent extension of the mean--field approach can be used in particular to shed light on nuclear shape properties, particularly looking at the giant resonances built on deformed nuclear ground states, and at dynamics in highly-deformed fission isomers. Example calculations are shown of $^{28}$Si in the first case, and $^{240}$Pu in the latter case.Comment: 9 pages, 5 figures, to appear in proceedings of International Workshop "Shapes and Dynamics of Atomic Nuclei: Contemporary Aspects" (SDANCA-15), 8-10 October 2015, Sofia, Bulgari

Cause of the charge radius isotope shift at the \emph{N}=126 shell gap

We discuss the mechanism causing the `kink' in the charge radius isotope shift at the N=126 shell closure. The occupation of the 1$i_{11/2}$ neutron orbital is the decisive factor for reproducing the experimentally observed kink. We investigate whether this orbital is occupied or not by different Skyrme effective interactions as neutrons are added above the shell closure. Our results demonstrate that several factors can cause an appreciable occupation of the 1$i_{11/2}$ neutron orbital, including the magnitude of the spin-orbit field, and the isoscalar effective mass of the Skyrme interaction. The symmetry energy of the effective interaction has little influence upon its ability to reproduce the kink.Comment: 4 pages, 4 figures, to be submitted to proceedings of INPC 201

Lancifodilactone G : insights about an unusually stable enol

From quantum mechanics calculations we confirm that the naturally occurring enol lancifodilactone G is stable over the keto form (by 2.6 kcal/mol in water), the only known stable aliphatic enol (devoid of conjugated or bulky aromatics and lacking a 1,3-diketone structural motif known to stabilize enols). We determine architectural elements responsible for the enol stabilization and find a mechanism for keto-enol conversion in solution. In addition, we correct previously reported computational results that were performed on the misinterpreted structure demonstrating that the enol form of this natural product is more stable than previously thought

Predictions of structural elements for the binding of Hin recombinase with the hix site of DNA

Molecular dynamics simulations were coupled with experimental data from biochemistry and genetics to generate a theoretical structure for the binding domain of Hin recombinase complexed with the hix site of DNA. The theoretical model explains the observed sequence specificity of Hin recombinase and leads to a number of testable predictions concerning altered sequence selectivity for various mutants of protein and DNA. Combining molecular dynamics simulations with constraints based on current knowledge of protein structure leads to a theoretical structure of the binding domain of Hin recombinase with the hix site of DNA. The model offers a mechanistic explanation of the presently known characteristics of Hin and predicts the effects of specific mutations of both protein and DNA. The predictions can be tested by currently feasible experiments that should lead to refinements in and improvements on the current theoretical model. Because current experimental and theoretical methods are all limited to providing only partial information about protein-DNA interactions, we believe that this approach of basing molecular simulations on experimental knowledge and using the results of these simulations to design new, more precise experimental tests will be of general utility. These results provide additional evidence for the generality of the helix-turn-helix motif in DNA recognition and stabilization of proteins on DNA

A Multiscale Approach for Modeling Crystalline Solids

In this paper we present a modeling approach to bridge the atomistic with macroscopic scales in crystalline materials. The methodology combines identification and modeling of the controlling unit processes at microscopic level with the direct atomistic determination of fundamental material properties. These properties are computed using a many body Force Field derived from ab initio quantum-mechanical calculations. This approach is exercised to describe the mechanical response of high-purity Tantalum single crystals, including the effect of temperature and strain-rate on the hardening rate. The resulting atomistically informed model is found to capture salient features of the behavior of these crystals such as: the dependence of the initial yield point on temperature and strain rate; the presence of a marked stage I of easy glide, specially at low temperatures and high strain rates; the sharp onset of stage II hardening and its tendency to shift towards lower strains, and eventually disappear, as the temperature increases or the strain rate decreases; the parabolic stage II hardening at low strain rates or high temperatures; the stage II softening at high strain rates or low temperatures; the trend towards saturation at high strains; the temperature and strain-rate dependence of the saturation stress; and the orientation dependence of the hardening rate.Comment: 25 pages, 15 figures, LaTe