Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices.

Nonlinear optical effects manifested by electromagnetic induced transparency in cold atoms

This dissertation reports experimental studies of nonlinear optical effects manifested by electromagnetically induced transparency (EIT) in cold Rb atoms. The cold Rb atoms are confined in a magneto-optic trap (MOT) obtained with the standard laser cooling and trapping technique. Because of the near zero Doppler shift and a high phase density, the cold Rb sample is well suited for studies of atomic coherence and interference and related applications, and the experiments can be compared quantitatively with theoretical calculations. It is shown that with EIT induced in the multi-level Rb system by laser fields, the linear absorption is suppressed and the nonlinear susceptibility is enhanced, which enables studies of nonlinear optics in the cold atoms with slow photons and at low light intensities. Three independent experiments are described and the experimental results are presented. First, an experimental method that can produce simultaneously co-propagating slow and fast light pulses is discussed and the experimental demonstration is reported. Second, it is shown that in a three-level Rb system coupled by multi-color laser fields, the multi-channel two-photon Raman transitions can be manipulated by the relative phase and frequency of a control laser field. Third, a scheme for all-optical switching near single photon levels is developed. The scheme is based on the phase-dependent multi-photon interference in a coherently coupled four-level system. The phase dependent multi-photon interference is observed and switching of a single light pulse by a control pulse containing ∼20 photons is demonstrated. These experimental studies reveal new phenomena manifested by quantum coherence and interference in cold atoms, contribute to the advancement of fundamental quantum optics and nonlinear optics at ultra-low light intensities, and may lead to the development of new techniques to control quantum states of atoms and photons, which will be useful for applications in quantum measurements and quantum photonic devices.

Yield of metastable atoms from a rare gas discharge in a longitudinal magnetic field

Atomic beam experiments are limited by intensity. Intensity limitations are specially critical in the measurements of metastable atoms, since their relative population is several order of magnitude smaller than the beam population. This thesis provides a method for increasing the intensity of metastable argon and neon beams effusing from a hot cathode, glow discharge by use of a longitudinal magnetic field. The argon and neon metastable atom intensities have been measured for a range of discharge pressure, voltage, and current for a magnetic field strengths from 0 to 31 mT. For both argon and neon, the metastable atom beam intensity rises to a maximum value about one order of magnitude above the zero field case. A qualitative discussion of the theory of this phenomenon is also presented.

Generalized atoms in molecules approach (GAIM approach)

This thesis involves two parts. The first is a new-proposed theoretical approach called generalized atoms in molecules (GAIM). The second is a computational study on the deamination reaction of adenine with OH⁻/nH₂O (n=0, 1, 2, 3) and 3H₂O. The GAIM approach aims to solve the energy of each atom variationally in the first step and then to build the energy of a molecule from each atom. Thus the energy of a diatomic molecule (A-B) is formulated as a sum of its atomic energies, EA and EB. Each of these atomic energies is expressed as, EA = Hᴬ + Vₑₑᴬᴬ + 1/2Vₑₑᴬ<>ᴮ EB = Hᴮ + Vₑₑᴮᴮ + 1/2Vₑₑᴬ<>ᴮ where; Hᴬ and Hᴮ are the kinetic and nuclear attraction energy of electrons of atoms A and B, respectively; Vₑₑᴬᴬ and Vₑₑᴮᴮ are the interaction energy between the electrons on atoms A and B, respectively; and Vₑₑᴬ<>ᴮ is the interaction energy between the electrons of atom A with the electrons of atom B. The energy of the molecule is then minimized subject to the following constraint, |ρA(r)dr + |ρB(r)dr = N where ρA(r) and ρB(r) are the electron densities of atoms A and B, respectively, and N is the number of electrons. The initial testing of the performance of GAIM was done through calculating dissociation curves for H₂, LiH, Li₂, BH, HF, HCl, N₂, F₂, and Cl₂. The numerical results show that GAIM performs very well with H₂, LiH, Li₂, BH, HF, and HCl. GAIM shows convergence problems with N₂, F₂, and Cl₂ due to difficulties in reordering the degenerate atomic orbitals Pₓ, Py, and Pz in N, F, and Cl atoms. Further work for the development of GAIM is required. Deamination of adenine results in one of several forms of premutagenic lesions occurring in DNA. In this thesis, mechanisms for the deamination reaction of adenine with OH⁻/nH₂O, (n = 0, 1, 2, 3) and 3H₂O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to optimize all the geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH⁻/nH₂O and 3H₂O. The first four pathways (A-D) begin with by deprotonation at the amino group of adenine by OH⁻, while pathway E is initiated by tautomerization of adenine. For all pathways, the next two steps involve the formation of a tetrahedral intermediate followed by dissociation to yield products via a 1,3-hydrogen shift. Deamination with a single OH⁻ has a high activation barrier (190 kJ mol⁻¹ using G3MP2B3 level) for the rate-determining step. Addition of one water molecule reduces this barrier by 68 kJ mol⁻¹ calculated at G3MP2B3 level. Adding more water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H₂O, which has an overall G3MP2B3 activation energy of 139 and 137 kJ mol⁻¹ in the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH⁻/3H₂O by 6 and 2 kJ mol⁻¹ in the gas phase and PCM, respectively.

Nonlinear optics with cold Rb atoms using tapered optical nanofibres

Optical nanofibres (ONFs) are very thin optical waveguides with sub-wavelength diameters. ONFs have very high evanescent fields and the guided light is confined strongly in the transverse direction. These fibres can be used to achieve strong light-matter interactions. Atoms around the waist of an ONF can be probed by collecting the atomic fluorescence coupling or by measuring the transmission (or the polarisation) of the probe beam sent through it. This thesis presents experiments using ONFs for probing and manipulating laser-cooled 87Rb atoms. As an initial experiment, a single mode ONF was integrated into a magneto-optical trap (MOT) and used for measuring the characteristics of the MOT, such as the loading time and the average temperature of the atom cloud. The effect of a near-resonant probe beam on the local temperature of the cold atoms has been studied. Next, the ONF was used for manipulating the atoms in the evanescent fields region in order to generate nonlinear optical effects. Four-wave mixing, ac Stark effect (Autler-Townes splitting) and electromagnetically induced transparency have been observed at unprecedented ultralow power levels. In another experiment, a few-mode ONF, supporting only the fundamental mode and the first higher order mode group, has been used for studying cold atoms. A higher pumping rate of the atomic fluorescence into the higher order fibreguided modes and more interactions with the surrounding atoms for higher order mode evanescent light, when compared to signals for the fundamental mode, have been identified. The results obtained in the thesis are particularly for a fundamental understanding of light-atom interactions when atoms are near a dielectric surface and also for the development of fibre-based quantum information technologies. Atoms coupled to ONFs could be used for preparing intrinsically fibre-coupled quantum nodes for quantum computing and the studies presented here are significant for a detailed understanding of such a system.

Temperature measurement of cold atoms using transient absorption of a resonant probe through an optical nanofibre

Optical nanofibres are ultrathin optical fibres with a waist diameter typically less than the wavelength of light being guided through them. Cold atoms can couple to the evanescent field of the nanofibre-guided modes and such systems are emerging as promising technologies for the development of atom-photon hybrid quantum devices. Atoms within the evanescent field region of an optical nanofibre can be probed by sending near or on-resonant light through the fibre; however, the probe light can detrimentally affect the properties of the atoms. In this paper, we report on the modification of the local temperature of laser-cooled 87Rb atoms in a magneto-optical trap centred around an optical nanofibre when near-resonant probe light propagates through it. A transient absorption technique has been used to measure the temperature of the affected atoms and temperature variations from 160 μk to 850 μk, for a probe power ranging from 0 to 50 nW, have been observed. This effect could have implications in relation to using optical nanofibres for probing and manipulating cold or ultracold atoms.

van der Waals coefficients for positronium interactions with atoms

The random-phase approximation with exchange (RPAE) is used with a B-spline basis to compute dynamic dipole polarizabilities of noble-gas atoms and several other closed-shell atoms (Be, Mg, Ca, Zn, Sr, Cd, and Ba). From these, values of the van der Waals C₆ constants for positronium interactions with these atoms are determined and compared with existing data. After correcting the RPAE polarizabilities to fit the most accurate static polarizability data, our best predictions of C₆ for Ps–noble-gas pairs are expected to be accurate to within 1%, and to within a few percent for the alkaline-earth metals. We also used accurate dynamic dipole polarizabilities from the literature to compute the C₆ coefficients for the alkali-metal atoms. Implications of increased C₆ values for Ps scattering from more polarizable atoms are discussed.

Positronium collisions with rare-gas atoms

We calculate elastic scattering of positronium (Ps) by the Xe atom using the recently developed pseudopotential method (Fabrikant and Gribakin 2014 Phys. Rev. A 90 052717) and review general features of Ps scattering from heavier rare-gas atoms: Ar, Kr and Xe. The total scattering cross section is dominated by two contributions: elastic scattering and Ps ionization (break-up). To calculate the Ps ionization cross sections we use the binary-encounter method for Ps collisions with an atomic target. Our results for the ionization cross section agree well with previous calculations carried out in the impulse approximation. Our total Ps–Xe cross section, when plotted as a function of the projectile velocity, exhibits similarity with the electron-Xe cross section for the collision velocities higher than 0.8 a.u., and agrees very well with the measurements at Ps velocities above 0.5 a.u.

Formation of positron-atom bound states in collisions between Rydberg Ps and neutral atoms

Predicted 20 years ago, positron binding to neutral atoms has not yet been observed experimentally. A scheme is proposed to detect positron-atom bound states by colliding Rydberg positronium (Ps) with neutral atoms. Estimates of the charge-transfer reaction cross section are obtained using the first Born approximation for a selection of neutral atom targets and a wide range of incident Ps energies and principal quantum numbers. We also estimate the corresponding Ps ionization cross section. The accuracy of the calculations is tested by comparison with earlier predictions for charge transfer in Ps collisions with hydrogen and antihydrogen. We describe an existing Rydberg Ps beam suitable for producing positron-atom bound states and estimate signal rates based on the calculated cross sections and realistic experimental parameters. We conclude that the proposed methodology is capable of producing such states and of testing theoretical predictions of their binding energies.

Ionization of Atoms by Slow Heavy Particles, Including Dark Matter

Atoms and molecules can become ionized during the scattering of a slow, heavy particle off a bound electron. Such an interaction involving leptophilic weakly interacting massive particles (WIMPs) is a promising possible explanation for the anomalous 9σ annual modulation in the DAMA dark matter direct detection experiment [R. Bernabei et al., Eur. Phys. J. C 73, 2648 (2013)]. We demonstrate the applicability of the Born approximation for such an interaction by showing its equivalence to the semiclassical adiabatic treatment of atomic ionization by slow-moving WIMPs. Conventional wisdom has it that the ionization probability for such a process should be exponentially small. We show, however, that due to nonanalytic, cusplike behavior of Coulomb functions close to the nucleus this suppression is removed, leading to an effective atomic structure enhancement. We also show that electron relativistic effects actually give the dominant contribution to such a process, enhancing the differential cross section by up to 1000 times.

Position-dependent spin-orbit coupling for ultracold atoms

We theoretically explore atomic Bose-Einstein condensates (BECs) subject to position-dependent spin-orbit coupling (SOC). This SOC can be produced by cyclically laser coupling four internal atomic ground (or metastable) states in an environment where the detuning from resonance depends on position. The resulting spin-orbit coupled BEC (SOBEC) phase separates into domains, each of which contain density modulations-stripes-aligned either along the x or y direction. In each domain, the stripe orientation is determined by the sign of the local detuning. When these stripes have mismatched spatial periods along domain boundaries, non-trivial topological spin textures form at the interface, including skyrmions-like spin vortices and anti-vortices. In contrast to vortices present in conventional rotating BECs, these spin-vortices are stable topological defects that are not present in the corresponding homogenous stripe-phase SOBECs.

Resonant five-body recombination in an ultracold gas of bosonic atoms

We combine theory and experiment to investigate five-body recombination in an ultracold gas of atomic cesium at negative scattering length. A refined theoretical model, in combination with extensive laboratory tunability of the interatomic interactions, enables the five-body resonant recombination rate to be calculated and measured. The position of the new observed recombination feature agrees with a recent theoretical prediction and supports the prediction of a family of universal cluster states at negative a that are tied to an Efimov trimer.