The Li-8(p, alpha)He-5 reaction at low energies, and Be-9 spectroscopy around the proton threshold

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Topics in equilibrium and nonequilibrium thermodynamics: computing crystalline free energies and engineering Maxwell’s demon.

This dissertation covers two separate topics in statistical physics. The first part of the dissertation focuses on computational methods of obtaining the free energies (or partition functions) of crystalline solids. We describe a method to compute the Helmholtz free energy of a crystalline solid by direct evaluation of the partition function. In the many-dimensional conformation space of all possible arrangements of N particles inside a periodic box, the energy landscape consists of localized islands corresponding to different solid phases. Calculating the partition function for a specific phase involves integrating over the corresponding island. Introducing a natural order parameter that quantifies the net displacement of particles from lattices sites, we write the partition function in terms of a one-dimensional integral along the order parameter, and evaluate this integral using umbrella sampling. We validate the method by computing free energies of both face-centered cubic (FCC) and hexagonal close-packed (HCP) hard sphere crystals with a precision of $10^{-5}k_BT$ per particle. In developing the numerical method, we find several scaling properties of crystalline solids in the thermodynamic limit. Using these scaling properties, we derive an explicit asymptotic formula for the free energy per particle in the thermodynamic limit. In addition, we describe several changes of coordinates that can be used to separate internal degrees of freedom from external, translational degrees of freedom. The second part of the dissertation focuses on engineering idealized physical devices that work as Maxwell's demon. We describe two autonomous mechanical devices that extract energy from a single heat bath and convert it into work, while writing information onto memory registers. Additionally, both devices can operate as Landauer's eraser, namely they can erase information from a memory register, while energy is dissipated into the heat bath. The phase diagrams and the efficiencies of the two models are solved and analyzed. These two models provide concrete physical illustrations of the thermodynamic consequences of information processing.

Universality of weakly bound dimers and Efimov trimers close to Li-Cs Feshbach resonances

We study the interspecies scattering properties of ultracold Li-Cs mixtures in their two energetically lowest spin channels in the magnetic field range between 800 and 1000 G. Close to two broad Feshbach resonances (FR) we create weakly bound LiCs dimers by radio-frequency association and measure the dependence of their binding energy on the external magnetic field strength. Based on the binding energies and complementary atom loss spectroscopy of three other Li-Cs s-wave FRs we construct precise molecular singlet and triplet electronic ground state potentials using a coupled-channels calculation. We extract the Li-Cs interspecies scattering length as a function of the external field and obtain almost a ten-fold improvement in the precision of the values for the pole positions and widths of the s-wave FRs as compared to our previous work (Pires et al 2014 Phys. Rev. Lett. 112 250404). We discuss implications on the Efimov scenario and the universal geometric scaling for LiCsCs trimers.

Effect of functional groups on separating carbon dioxide from CO2/N-2 gas mixtures using edge functionalized graphene nanoribbons

Development of microporous adsorbents for separation and sequestration of carbon dioxide from flue gas streams is an area of active research. In this study, we assess the influence of specific functional groups on the adsorption selectivity of CO2/N-2 mixtures through Grand Canonical Monte Carlo (GCMC) simulations. Our model system consists of a bilayer graphene nanoribbon that has been edge functionalized with OH, NH2, NO2, CH3 and COOH. Ab initio Moller-Plesset (MP2) calculations with functionalized benzenes are used to obtain binding energies and optimized geometries for CO2 and N-2. This information is used to validate the choice classical forcefields in GCMC simulations. In addition to simulations of adsorption from binary mixtures of CO2 and N-2, the ideal adsorbed solution theory (IAST) is used to predict mixture isotherms. Our study reveals that functionalization always leads to an increase in the adsorption of both CO2 and N-2 with the highest for COOH. However, significant enhancement in the selectivity for CO2 is only seen with COOH functionalized nanoribbons. The COOH functionalization gives a 28% increase in selectivity compared to H terminated nanoribbons, whereas the improvement in the selectivity for other functional groups are much Enure modest. Our study suggests that specific functionalization with COOH groups can provide a material's design strategy to improve CO2 selectivity in microporous adsorbents. Synthesis of graphene nanoplatelets with edge functionalized COOH, which has the potential for large scale production, has recently been reported (Jeon el, al., 2012). (C) 2014 Elsevier Ltd. All rights reserved,

Nuclear Hartree-Fock calculations on parallel computers

Hartree-Fock (HF) calculations have had remarkable success in describing large nuclei at high spin, temperature and deformation. To allow full range of possible deformations, the Skyrme HF equations can be discretized on a three-dimensional mesh. However, such calculations are currently limited by the computational resources provided by traditional supercomputers. To take advantage of recent developments in massively parallel computing technology, we have implemented the LLNL Skyrme-force static and rotational HF codes on Intel's DELTA and GAMMA systems at Caltech.

We decomposed the HF code by assigning a portion of the mesh to each node, with nearest neighbor meshes assigned to nodes connected by communication· channels. This kind of decomposition is well-suited for the DELTA and the GAMMA architecture because the only non-local operations are wave function orthogonalization and the boundary conditions of the Poisson equation for the Coulomb field.

Our first application of the HF code on parallel computers has been the study of identical superdeformed (SD) rotational bands in the Hg region. In the last ten years, many SD rotational bands have been found experimentally. One very surprising feature found in these SD rotational bands is that many pairs of bands in nuclei that differ by one or two mass units have nearly identical deexcitation gamma-ray energies. Our calculations of the five rotational bands in ^(192)Hg and ^(194)Pb show that the filling of specific orbitals can lead to bands with deexcitation gamma-ray energies differing by at most 2 keV in nuclei differing by two mass units and over a range of angular momenta comparable to that observed experimentally. Our calculations of SD rotational bands in the Dy region also show that twinning can be achieved by filling or emptying some specific orbitals.

The interpretation of future precise experiments on atomic parity nonconservation (PNC) in terms of parameters of the Standard Model could be hampered by uncertainties in the atomic and nuclear structure. As a further application of the massively parallel HF calculations, we calculated the proton and neutron densities of the Cesium isotopes from A = 125 to A = 139. Based on our good agreement with experimental charge radii, binding energies, and ground state spins, we conclude that the uncertainties in the ratios of weak charges are less than 10^(-3), comfortably smaller than the anticipated experimental error.

Sequence-function relationships in E. coli transcriptional regulation

Understanding how transcriptional regulatory sequence maps to regulatory function remains a difficult problem in regulatory biology. Given a particular DNA sequence for a bacterial promoter region, we would like to be able to say which transcription factors bind there, how strongly they bind, and whether they interact with each other and/or RNA polymerase, with the ultimate objective of integrating knowledge of these parameters into a prediction of gene expression levels. The theoretical framework of statistical thermodynamics provides a useful framework for doing so, enabling us to predict how gene expression levels depend on transcription factor binding energies and concentrations. We used thermodynamic models, coupled with models of the sequence-dependent binding energies of transcription factors and RNAP, to construct a genotype to phenotype map for the level of repression exhibited by the lac promoter, and tested it experimentally using a set of promoter variants from E. coli strains isolated from different natural environments. For this work, we sought to ``reverse engineer'' naturally occurring promoter sequences to understand how variations in promoter sequence affects gene expression. The natural inverse of this approach is to ``forward engineer'' promoter sequences to obtain targeted levels of gene expression. We used a high precision model of RNAP-DNA sequence dependent binding energy, coupled with a thermodynamic model relating binding energy to gene expression, to predictively design and verify a suite of synthetic E. coli promoters whose expression varied over nearly three orders of magnitude.

However, although thermodynamic models enable predictions of mean levels of gene expression, it has become evident that cell-to-cell variability or ``noise'' in gene expression can also play a biologically important role. In order to address this aspect of gene regulation, we developed models based on the chemical master equation framework and used them to explore the noise properties of a number of common E. coli regulatory motifs; these properties included the dependence of the noise on parameters such as transcription factor binding strength and copy number. We then performed experiments in which these parameters were systematically varied and measured the level of variability using mRNA FISH. The results showed a clear dependence of the noise on these parameters, in accord with model predictions.

Finally, one shortcoming of the preceding modeling frameworks is that their applicability is largely limited to systems that are already well-characterized, such as the lac promoter. Motivated by this fact, we used a high throughput promoter mutagenesis assay called Sort-Seq to explore the completely uncharacterized transcriptional regulatory DNA of the E. coli mechanosensitive channel of large conductance (MscL). We identified several candidate transcription factor binding sites, and work is continuing to identify the associated proteins.

Double ionization of atomic negative ions in an intense laser field

In recent years there have been many studies of multiple ionization of closed shell rare gas atoms by intense laser fields. Until now no similar work has been done in the study of more diverse targets such as negative ions where low binding energies and strong electron correlations could yield distinctive behaviour. We present the first results of ionization of more than one electron from a range of atomic negative ions by intense laser pulses. Although these pulses are long by modern standards, and tend to produce sequential ionization in atoms, the positive ion yields from the negative ions do not depend predictably on the ionization potentials. This suggests that there may, intriguingly, be an alternative mechanism enhancing double ionization at low intensities.

Strong parallel magnetic field effects on the hydrogen molecular ion

Equilibrium distances, binding energies and dissociation energies for the ground and low-lying states of the hydrogen molecular ion in a strong magnetic field parallel to the internuclear axis are calculated and refined, by using the two- dimensional pseudospectral method. High-precision results are presented for the binding energies over a wider field regime than already given in the literature (Kravchenko and Liberman 1997 Phys. Rev. A 55 2701). The present work removes a long- standing discrepancy for the R-eq value in the 1sigma(u) state at a field strength of 1.0 x 10(6) T. The dissociation energies of the antibonding 1pi(g) state induced by magnetic fields are determined accurately. We have also observed that the antibonding 1pi(g) potential energy curve develops a minimum if the field is sufficiently strong. Some unreliable results in the literature are pointed out and discussed. A way to efficiently treat vibrational processes and coupling between the nuclear and the electronic motions in magnetic fields is also suggested within a three-dimensional pseudospectral scheme.

Site symmetry dependence of repulsive interactions between chemisorbed oxygen atoms on Pt{100}-(1x1)

Ab initio total energy calculations using density functional theory with the generalized gradient approximation have been performed for the chemisorption of oxygen atoms on a Pt{100}-(1 x 1) slab. Binding energies for the adsorption of oxygen on different high-symmetry sites are presented. The bridge site is the most stable at a coverage of 0.5 ML, followed by the fourfold hollow site. The atop site is the least stable. This finding is rationalized by analyzing the ''local structures'' formed upon oxygen chemisorption. The binding energies and heats of adsorption at different oxygen coverages show that pairwise repulsive interactions are considerably stronger between oxygen atoms occupying fourfold sites than those occupying bridge sites. Analysis of the partial charge densities associated with Bloch states demonstrates that the O-Pt bond is considerably more localized at the bridge site. These effects cause a sharp drop in the heats of adsorption for oxygen on hollow sites when the coverage is increased from 0.25 to 0.5 ML. Mixing between oxygen p orbitals and Pt d orbitals can be observed over the whole metal d-band energy range.

Molecular dynamics simulations of proteins: can the explicit water model be varied?

In molecular mechanics simulations of biological systems, the solvation water is typically represented by a default water model which is an integral part of the force field. Indeed, protein nonbonding parameters are chosen in order to obtain a balance between water-water and protein-water interactions and hence a reliable description of protein solvation. However, less attention has been paid to the question of whether the water model provides a reliable description of the water properties under the chosen simulation conditions, for which more accurate water models often exist. Here we consider the case of the CHARMM protein force field, which was parametrized for use with a modified TIP3P model. Using quantum mechanical and molecular mechanical calculations, we investigate whether the CHARMM force field can be used with other water models: TIP4P and TIP5P. Solvation properties of N-methylacetamide (NMA), other small solute molecules, and a small protein are examined. The results indicate differences in binding energies and minimum energy geometries, especially for TIP5P, but the overall description of solvation is found to be similar for all models tested. The results provide an indication that molecular mechanics simulations with the CHARMM force field can be performed with water models other than TIP3P, thus enabling an improved description of the solvent water properties.

Kondo-attractive-Hubbard model for the ordering of local magnetic moments in superconductors

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estrutura de sistemas de três corpos fracamente ligados em duas dimensões

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Atomistic Modeling of Effect of Mg on Oxygen Vacancy Diffusion in α-Alumina

Oxygen diffusion plays an important role in grain growth and densification during the sintering of alumina ceramics and governs high-temperature processes such as creep. The atomistic mechanism for oxygen diffusion in alumina is, however, still debated; atomistic calculations not being able to match experimentally determined activation energies for oxygen vacancy diffusion. These calculations are, however, usually performed for perfectly pure crystals, whereas virtually every experimental alumina sample contains a significant fraction of impurity/dopants ions. In this study, we use atomistic defect cluster and nudged elastic band (NEB) calculations to model the effect of Mg impurities/dopants on defect binding energies and migration barriers. We find that oxygen vacancies can form energetically favorable clusters with Mg, which reduces the number of mobile species and leads to an additional 1.5 eV energy barrier for the detachment of a single vacancy from Mg. The migration barriers of diffusive jumps change such that an enhanced concentration of oxygen vacancies is expected around Mg ions. Mg impurities were also found to cause destabilization of certain vacancy configurations as well as enhanced vacancy–vacancy interaction.