Energy Ground State Research Articles

Fluorescence from an H-aggregated naphthalenediimide based peptide: photophysical and computational investigation of this rare phenomenon.

Fluorescence associated with J-aggregated naphthalenediimides (NDIs) is common. However, in this study an NDI based synthetic peptide molecule is found to form a fluorescent H-aggregate in a chloroform (CHCl3)-methylcyclohexane (MCH) mixture. An attempt has been made to explain the unusual fluorescence property of this H-aggregated NDI derivative. Time correlated single photon counting (TCSPC) shows that the average lifetime of the NDI based molecule is on the order of a few nanoseconds. It is revealed from the computational study that the transition from the second exited state (S2) to the ground energy state (S0) is responsible for the fluorescence as S1 is a dark state. Such rare violation of Kasha's rule accounts for the unusual fluorescence properties of this type of NDI molecule in the H-aggregated state.

Dynamics of a Naturally Hidden State Restricts Adenylate Kinase Activity

Enzymes are extraordinary biocatalysts that accelerate chemical reactions by performing several complex tasks simultaneously including; (1) binding of substrates weakly enough to avoid thermodynamic pits; (2) extremely tight binding to the transition state compound; (3) activation of functional groups on the substrate(s) and (4) dehydration of active sites. These tasks are often associated with conformational changes and therefore conformational dynamics is by definition crucial for enzymatic function. An emerging paradigm in enzymology is that dynamically accessed transient high-energy structural states are fundamental entities for enzymatic reaction cycles. These high-energy or “invisible” states are not possible to study directly at atomic resolution with existing spectroscopic techniques because their low relative populations and residence times. Here, we have been able to cool down the rate of conformational dynamics of an adenylate kinase (AK) variant to the extent that a high energy ligand-bound state becomes directly observable with solution state NMR spectroscopy. It was found that the catalytic activity of the enzyme is restricted by the dynamic interconversion between the high energy state and a low energy ground state. In complete agreement with the presented catalytic model is was found that the energetic barrier for the catalytic function, as probed with a functional assay, is of the same magnitude as the barrier for conformational dynamics. Our work shows that it is possible to tune the rate constants of conformational dynamics resulting in a predictable perturbation of the enzymatic activity.

On the temperature dependence of silicon quantum dot photoluminescence

A model of radiative and nonradiative transitions in silicon quantum dots is presented, which describes the photoluminescence temperature dependence of the ion-synthesized ensembles of Si nanocrystals in SiO2. A four-level system of transitions is considered that takes into account thermally activated processses and exchange splitting of the ground energy state of exciton in a silicon nanocrystal into triplet and singlet levels, the transfers from which to the ground state are responsible for the luminescence. The temperature dependence of monochromatic photoluminescence components was obtained based on the stationary solution of the system of kinetic equations for the population of levels that satisfactory describes the experimental data. The exciton energy splitting values depending on the energy of emitted photons were found and compared with the data in the literature.

Domain-Wall-Assisted Switching of Chains of Coupled Nanomagnets

We experimentally demonstrate that the stray field of a propagating transverse domain wall can switch chains of coupled nanomagnets (nanomagnet wires) to a magnetically ordered, low energy ground state. We fabricated nanomagnet wires consisting of 6 and 20 nanomagnets that were placed adjacent to a domain-wall conductor. Magnetic force microscope images clearly show the nanomagnet wire switching from an initial metastable state to an ordered ground state. This can be exploited for controlled order of nanomagnet switching and for energy-efficient clocking of nanomagnet logic devices. Reference structures were fabricated and characterized to prove our assumptions.

First principles calculations of the magnetic and hyperfine properties of Fe/N/Fe and Fe/O/Fe multilayers in the ground state of cohesive energy

The ground state properties of Fe/N/Fe and Fe/O/Fe multilayers were investigated using the first principles calculations. The calculations were performed using the Linearized Augmented Plane Wave (LAPW) method implemented in the Wien2k code. A supercell consisting of one layer of nitride (or oxide) between two layers of Fe in the bcc structure was used to model the structure of the multilayer. The research in new materials also stimulated theoretical and experimental studies of iron-based nitrides due to their variety of structural and magnetic properties for the potential applications as in high strength steels and for high corrosion resistance. It is obvious from many reports that magnetic iron nitrides such as γ-Fe4N and α-Fe16N2 have interesting magnetic properties, among these a high magnetisation saturation and a high density crimp. However, although Fe–N films and multilayers have many potential applications, they can be produced in many ways and are being extensively studied from the theoretical point of view there is no detailed knowledge of their electronic structure. Clearly, efforts to understand the influence of the nitrogen atoms on the entire electronic structure are needed as to correctly interpret the observed changes in the magnetic properties when going from Fe–N bulk compounds to multilayer structures.Nevertheless, the N atoms are not solely responsible for electronics alterations in solid compounds. Theoretical results showed that Fe4X bulk compounds, where X is a variable atom with increasing atomic number (Z), the nature of bonding between X and adjacent Fe atoms changes from more covalent to more ionic and the magnetic moments of Fe also increase for Z=7, i.e. N. This is an indicative that atoms with a Z number higher than 7, i.e., O, can produce several new alterations in the entire magnetic properties of Fe multilayers.This paper presents the first results of an ab-initio electronic structure calculations, performed for Fe–N and Fe–O multilayers. Firstly, the formation energy and the cohesive energy of the multilayers are discussed. For optimised values, the cohesive energy of the multilayers to obtain the lattice parameters at the equilibrium ground state was used, i.e. a new methodology for this calculus was applied. Secondly, the magnetic properties and hyperfine interactions (magnetic field, electric field gradient and the isomer shift) of the iron atoms of the multilayers are discussed.

Data mechanics and coupling geometry on binary bipartite networks.

We quantify the notion of pattern and formalize the process of pattern discovery under the framework of binary bipartite networks. Patterns of particular focus are interrelated global interactions between clusters on its row and column axes. A binary bipartite network is built into a thermodynamic system embracing all up-and-down spin configurations defined by product-permutations on rows and columns. This system is equipped with its ferromagnetic energy ground state under Ising model potential. Such a ground state, also called a macrostate, is postulated to congregate all patterns of interest embedded within the network data in a multiscale fashion. A new computing paradigm for indirect searching for such a macrostate, called Data Mechanics, is devised by iteratively building a surrogate geometric system with a pair of nearly optimal marginal ultrametrics on row and column spaces. The coupling measure minimizing the Gromov-Wasserstein distance of these two marginal geometries is also seen to be in the vicinity of the macrostate. This resultant coupling geometry reveals multiscale block pattern information that characterizes multiple layers of interacting relationships between clusters on row and on column axes. It is the nonparametric information content of a binary bipartite network. This coupling geometry is then demonstrated to shed new light and bring resolution to interaction issues in community ecology and in gene-content-based phylogenetics. Its implied global inferences are expected to have high potential in many scientific areas.

Electron impact ionization cross sections for chloroethanes

The present work reports electron impact total ionization cross sections for chlorine substituted ethane molecules viz. C2H4Cl2, C2H3Cl3, C2H2Cl4, C2HCl5 and C2Cl6 in their gaseous ground state for the incident electron energies ranging from ionization threshold to 5keV. We have employed the spherical complex optical potential formalism and group additivity rule for the determination of inelastic cross sections. The total ionization cross section is derived from the total inelastic cross section using a semi-empirical method called complex scattering potential ionization contribution method. The results are compared with prior experimental and theoretical values wherever available and an overall reasonable agreement is found. In addition, a correlation is obtained between the maximum of ionization cross section versus the square root of the ratio of the polarisability to ionization potential.

Exploring vortex dynamics in the presence of dissipation: Analytical and numerical results

In the present work, we consider the problem of a system of few vortices $N \leq 5$ as it emerges from its experimental realization in the field of atomic Bose-Einstein condensates. Starting from the corresponding equations of motion, we use a two-pronged approach in order to reveal the configuration space of the system's preferred dynamical states. On the one hand, we use a Monte-Carlo method parametrizing the vortex "particles" by means of hyperspherical coordinates and identifying the minimal energy ground states thereof for $N=2, ..., 5$ and different vortex particle angular momenta. We then complement this picture with a dynamical systems analysis of the possible rigidly rotating states. The latter reveals all the supercritical and subcritical pitchfork, as well as saddle-center bifurcations that arise exposing the full wealth of the problem even at such low dimensional cases. By corroborating the results of the two methods, it becomes fairly transparent which branch the Monte-Carlo approach selects for different values of the angular momentum which is used as a bifurcation parameter.

TDDFT modeling of the CO‐photolysis of Fe2(S2C3H6)(CO)6, a model of the [FeFe]‐hydrogenase catalytic site

Upon irradiation with ultraviolet wavelengths, Fe2(S2C3H6)(CO)6, a simple model of the [FeFe]‐hydrogenase active site, undergoes CO dissociation to form the unsaturated Fe2(S2C3H6)(CO)5 species and successively a solvent adduct at the vacant coordination site. In the present work, the CO‐photolysis of Fe2(S2C3H6)(CO)6 was investigated by density functional theory (DFT) and time‐dependent DFT (TDDFT). Trans Fe2(S2C3H6)(CO)5 form and the corresponding trans heptane or acetonitrile solvent adducts are the lowest energy ground state forms. CO dissociation barriers computed for the lowest triplet state are roughly halved with respect to those for the ground state suggesting that some low‐lying excited potential energy surface (PES) could be loosely bound with respect to FeC bond cleavage. The TDDFT excited state PESs and geometry optimizations for the excited states likely involved in the CO‐photolysis suggest that the FeS bond elongation and the partial isomerization toward the rotated form could take place simultaneously, favoring the trans CO photodissociation. © 2014 Wiley Periodicals, Inc.

Packing of Softly Repulsive Particles in a Spherical Box—A Generalised Thomson Problem

We study the (near or close to) ground state distribution of N softly repelling particles trapped in the interior of a spherical box. The charges mutually interact via an inverse power law potential of the form 1/r γ .W estudy three regimes in which the charges form an single spherical shell at the edge of the box (γ = 1), a series of concentric shells of increasing density (γ = 2) and γ = 12 for which the charges form shells with a more uniform charge distribution. We conduct numerical simulations for clusters containing up to 5000 charges and compare charge density across the system with continuum limit results. The agreement between numerical (discrete) results and the continuum limit is found to improve with increasing N . These findings are accompanied by a visual gallery of some of the low energy ground states found by simulated annealing. Ke yw ords: Thomson Problem, Low Temperature Plasma, Packing in a Spherical Box

Exploring rigidly rotating vortex configurations and their bifurcations in atomic Bose-Einstein condensates

In the present work, we consider the problem of a system of few vortices N ≤ 5 as it emerges from its experimental realization in the field of atomic Bose-Einstein condensates. Starting from the corresponding equations of motion for an axially symmetric trapped condensate, we use a two-pronged approach in order to reveal the configuration space of the system's preferred dynamical states. We use a Monte Carlo method parametrizing the vortex particles by means of hyperspherical coordinates and identifying the minimal energy ground states thereof for N=2,...,5 and different vortex particle angular momenta. We then complement this picture with a dynamical system analysis of the possible rigidly rotating states. The latter reveals a supercritical and subcritical pitchfork, as well as saddle-center bifurcations that arise, exposing the full wealth of the problem even for such low-dimensional cases. By corroborating the results of the two methods, it becomes fairly transparent which branch the Monte Carlo approach selects for different values of the angular momentum that is used as a bifurcation parameter.

Theoretical study on excited-state intermolecular proton transfer reactions of 1H-pyrrolo[3,2-h]quinoline with water and methanol

The dynamics of the ultrafast excited-state multiple intermolecular proton transfer (PT) reactions in gas-phase complexes of 1H-pyrrolo[3,2-h]quinoline with water and methanol (PQ(H2O) n and PQ(MeOH) n , where n = 1, 2) is modeled using quantum-chemical simulations. The minimum energy ground-state structures of the complexes are determined. Molecular dynamics simulations in the first excited state are employed to determine reaction mechanisms and the time evolution of the PT processes. Excited-state dynamics results for all complexes reveal synchronous excited-state multiple proton transfer via solvent-assisted mechanisms along an intermolecular hydrogen-bonded network. In particular, excited-state double proton transfer is the most effective, occurring with the highest probability in the PQ(MeOH) cluster. The PT character of the reactions is suggested by nonexistence of crossings between ππ* and πσ* states.

Ground-state entanglement in coupled qubits

We study a system of qubits that are coupled to each other via only one degree of freedom represented, e.g., by $\sigma_z$-operators. We prove that, if by changing the Hamiltonian parameters, a non-degenerate ground state of the system is continuously transformed in such a way that the expectation values of $\sigma_z$ operators of at least two coupled qubits change, this ground state is entangled. Using this proof, we discuss connection between energy level anticrossings and ground state entanglement. Following the same line of thought, we introduce entanglement witnesses, based on cross-susceptibilities, that can detect ground state entanglement for any bipartition of the multi-qubit system. A witness for global ground state entanglement is also introduced.

Froth-like Minimizers of a Non-Local Free Energy Functional with Competing Interactions

We investigate the ground and low energy states of a one dimensional non local free energy functional describing at a mean field level a spin system with both ferromagnetic and antiferromagnetic interactions. In particular, the antiferromagnetic interaction is assumed to have a range much larger than the ferromagnetic one. The competition between these two effects is expected to lead to the spontaneous emergence of a regular alternation of long intervals on which the spin profile is magnetized either up or down, with an oscillation scale intermediate between the range of the ferromagnetic and that of the antiferromagnetic interaction. In this sense, the optimal or quasi-optimal profiles are "froth-like": if seen on the scale of the antiferromagnetic potential they look neutral, but if seen at the microscope they actually consist of big bubbles of two different phases alternating among each other. In this paper we prove the validity of this picture, we compute the oscillation scale of the quasi-optimal profiles and we quantify their distance in norm from a reference periodic profile. The proof consists of two main steps: we first coarse grain the system on a scale intermediate between the range of the ferromagnetic potential and the expected optimal oscillation scale; in this way we reduce the original functional to an effective "sharp interface" one. Next, we study the latter by reflection positivity methods, which require as a key ingredient the exact locality of the short range term. Our proof has the conceptual interest of combining coarse graining with reflection positivity methods, an idea that is presumably useful in much more general contexts than the one studied here.

H̄ and H̄+ production cross sections for the GBAR experiment

The production and cooling of the H̄+ ion is the key point of the GBAR experiment (Gravitational Behaviour of Antihydrogen at Rest), which aims at performing the free fall of antihydrogen atoms to measure ḡ, the acceleration of antimatter on Earth. H̄+ ions will be obtained from collisions between a positronium cloud and antiprotons delivered by the AD/ELENA facility at CERN, with intermediate formation of antihydrogen atoms. In order to optimise the experimental production of H̄+ ions, we computed the total cross sections of the two corresponding reactions, within the same theoretical framework of the Continuum Distorted Wave – Final State (CDW-FS) model. The different contributions of the H̄ excited states have been systematically investigated for different states of Ps. The results exhibit an increase of the H̄ production toward low kinetic energies, in agreement with experimental data and previous calculations, whereas the largest H̄+ production is obtained with low energy ground-state antihydrogen atoms. These theoretical predictions suggest that the overall production of H̄+ could be optimal for 2 keV antiproton impact energy, using positronium atoms prepared in the 2p state.

Non-Equilibrium Polar Localization of Proteins in Bacterial Cells

Many proteins are observed to localize to the poles within bacterial cells. Some bacteria show unipolar localization, yet under different conditions bipolar patterns can emerge. One mechanism for spontaneous polar localization has been shown to involve the combination of protein aggregation and nucleoid occlusion. Whether the different observed patterns represent global energy minima for the cellular system remains to be determined. In this paper we show that for a model consisting only of protein aggregation along with an excluded volume effect due to the DNA polymer, that unipolar patterns are the global energy ground state regardless of protein concentration and DNA density. We extend the model to allow for proteins to be added to the cellular volume at a constant rate and show that bipolar (or multi-foci) patterns emerge as the result of the system being kinetically trapped in a local energy minimum. Lastly we also consider the situation of a growing cell that starts with a pre-existing aggregate at one of the poles and determine conditions under which either unipolar or bipolar patterns can exist at the point when it is ready to divide. This work sheds new interpretations on recently published experimental data and suggests experiments to test whether such a mechanism can drive patterning in bacteria.

Polymerization Inhibition by Triplet State Absorption for Nanoscale Lithography

In the field of photopolymerization, multi-photon lithography1 stands out as a mask-free tool for fabricating three-dimensional structures inside a photocurable resin that is transparent at the wavelength used. This approach enables a great deal of versatility compared with single photon absorption lithography where the thickness of the polymerized parts is limited by the penetration depth of the light in the resin2 and therefore a layer-by-layer approach is necessary to fabricate 3D structures.3 The possibility of producing 3D, free-standing, and arbitrarily complex architectures opens up novel applications in various research fields, e.g., photonic crystals, metamaterials, and biological scaffold fabrication.4–10

Constrained energy minimization and ground states for NLS with point defects

We investigate the ground states of the one-dimensional nonlinear Schrödinger equationwith a defect located at a fixed point. The nonlinearity is focusing andconsists of a subcritical power. The notion of ground state can bedefined in several (often non-equivalent) ways. We define a ground state as a minimizer of the energyfunctional among the functions endowed with the same mass. This is the physically meaningful definition in the main fields of application of NLS.In this context we prove an abstract theorem that revisits theconcentration-compactness method and which is suitable to treat NLS with inhomogeneities. Then we apply it to three models,describing three different kinds of defect: delta potential, deltaprime interaction, and dipole. In the three cases we explicitly computeground states and we show their orbital stability.

Geometrical criteria versus quantum chemical criteria for assessment of intramolecular hydrogen bond (IMHB) interaction: A computational comparison into the effect of chlorine substitution on IMHB of salicylic acid in its lowest energy ground state conformer

Density functional theory based computational study has been performed to characterize intramolecular hydrogen bonding (IMHB) interaction in a series of salicylic acid derivatives varying in chlorine substitution on the benzene ring. The molecular systems studied are salicylic acid, 5-chlorosalicylic acid, 3,5-dichlorosalicylic acid and 3,5,6-tricholorosalicylic acid. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇2ρ(r) at the bond critical point using atoms-in-molecule theory. Topological features, energy densities based on ρ(r) through perturbing the intramolecular H-bond distances suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of covalent interaction. The interplay between aromaticity and resonance-assisted hydrogen bonding (RAHB) is discussed using both geometrical and magnetic criteria as the descriptors of aromaticity. The optimized geometry features, molecular electrostatic potential map analysis are also found to produce a consensus view in relation with the formation of RAHB in these systems.

Order and supersymmetry at high filling zero-energy states on the triangular lattice

We perform exact diagonalization studies in d=2 dimensions for the Fendley and Schoutens model of hard-core and nearest-neighbor excluding fermions that displays an exact non-relativistic supersymmetry. Using clusters of all possible shapes up to 46 sites, we systematically study the behavior of the ground state phase diagram as a function of filling. We focus on the highly degenerate zero-energy states found at fillings between 1/7 and ~1/5. At the lower end of that interval, at filling 1/7, we explicitly show that the ground states are gapped crystals. Consistent with previous suggestions, we find that the extensive entropy of zero states peaks at a filling of ~0.178. At the higher end of the interval, we find zero energy ground states at fillings above 1/5, in contradiction to previous numerical studies and analytical suggestions; these display non-trivial amplitude degeneracies.