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We present an accurate theoretical determination of rovibrational energy levels of the hydrogen molecule and its isotopologues in its electronic ground state. We consider all significant corrections to the Born-Oppenheimer approximation, obtained within nonadiabatic perturbation theory, including the mixed nonadiabatic-relativistic effects. Quantum electrodynamic corrections in the leading $\alpha^5\,m$ and the next-to-leading $\alpha^6\,m$ orders, as well as finite nuclear size effect, are also taken into account but within the Born-Oppenheimer approximation only. Final results for the transition wavelength between rovibrational levels achieve accuracy of the order of $10^{-3}$--$10^{-7}$ cm$^{-1}$, and are provided by simple to use computer code., Comment: 10 pages

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5′-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson–Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation (“Greek science” approach) or utilize information derived from known structures of other RNA molecules (“Babylonian science” approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately.

RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA–small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA–ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a “meta-predictor” leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl.

The thermal friction force acting on an atom moving relative to a thermal photon bath has recently been calculated on the basis of the fluctuation-dissipation theorem. The thermal fluctuations of the electromagnetic field give rise to a drag force on an atom provided one allows for dissipation of the field energy via spontaneous emission. The drag force exists if the atomic polarizability has a nonvanishing imaginary part. Here, we explore alternative derivations. The damping of the motion of a simple harmonic oscillator is described by radiative reaction theory (result of Einstein and Hopf), taking into account the known stochastic fluctuations of the electromagnetic field. Describing the excitations of the atom as an ensemble of damped harmonic oscillators, we identify the previously found expressions as generalizations of the Einstein-Hopf result. In addition, we present a simple explanation for blackbody friction in terms of a Doppler shift of the thermal radiation in the inertial frame of the moving atom: The atom absorbs blue-shifted photons from the front and radiates off energy in all directions, thereby losing energy. The original plus the two alternative derivations provide for additional confirmation of an intriguing quantum friction effect, and leave no doubt regarding its existence.

The dissociation energies from all rovibrational levels of H2 and D2 in the ground electronic state are calculated with high accuracy by including relativistic and quantum electrodynamics (QED) effects in the nonadiabatic treatment of the nuclear motion. For D2, the obtained energies have theoretical uncertainties of 0.001 cm(-1). For H2, similar uncertainties are for the lowest levels, while for the higher ones the uncertainty increases to 0.005 cm(-1). Very good agreement with recent high-resolution measurements of the rotational v = 0 levels of H2, including states with large angular momentum J, is achieved. This agreement would not have been possible without accurate evaluation of the relativistic and QED contributions and may be viewed as the first observation of the QED effects, mainly the electron self-energy, in a molecular spectrum. For several electric quadrupole transitions, we still observe certain disagreement with experimental results, which remains to be explained.

We analyze the NMR shielding constants in three isotopomers of the hydrogen molecule: H2, HD and D2. The results obtained within the Born–Oppenheimer approximation using the coupled-cluster singles-and-doubles model are very close to the previous theoretical values. In particular, the isotope shifts computed using significantly larger basis sets agree with the earlier literature results, confirming the disagreement of these calculations with the available experimental data. To examine the accuracy of the computed isotope shifts, we analyze in addition the relativistic corrections and estimate the role of the adiabatic and nonadiabatic effects. The relativistic corrections appear to be negligible; on the other hand, the changes in the shielding constants due to the adiabatic and nonadiabatic effects may account for the discrepancies between the computed and experimental isotope shifts.

We present a derivation of the finite nuclear mass corrections to the Casimir-Polder interaction between two atomic systems in the ground state. Equivalently, we show how the long-range asymptotics of the adiabatic correction is modified due to the finite speed of light. We show that in addition to the contribution resulting from the finite-mass correction to atomic polarizabilities, a further contribution exists.

The dissociation energy of molecular hydrogen is determined theoretically with a careful estimation of error bars by including nonadiabatic, relativistic, and quantum electrodynamics (QED) corrections. The relativistic and QED corrections were obtained at the adiabatic level of theory by including all contributions of the order α(2) and α(3) as well as the major (one-loop) α(4) term, where α is the fine-structure constant. The computed α(0), α(2), α(3), and α(4) components of the dissociation energy of the H2 isotopomer are 36 118.7978(2), -0.5319(3), -0.1948(2), and -0.0016(8) cm(-1), respectively, while their sum amounts to 36 118.0695(10) cm(-1), where the total uncertainty includes the estimated size (±0.0004 cm(-1)) of the neglected relativistic nonadiabatic/recoil corrections. The obtained theoretical value of the dissociation energy is in excellent agreement with the most recent experimental determination 36 118.0696(4) cm(-1) [J. Liu et al. J. Chem. Phys. 2009, 130, 174 306]. This agreement would have been impossible without inclusion of several subtle QED contributions which have not been considered, thus far, for molecules. A similarly good agreement is observed for the leading vibrational and rotational energy differences. For the D2 molecule we observe, however, a small disagreement between our value 36 748.3633(9) cm(-1) and the experimental result 36 748.343(10) cm(-1) obtained in a somewhat older and less precise experiment [Y. P. Zhang et al. Phys. Rev. Lett. 2004, 92, 203003]. The reason of this discrepancy is not known.

In the recent years, it has become clear that a wide range of regulatory functions in bacteria are performed by riboswitches--regions of mRNA that change their structure upon external stimuli. Riboswitches are therefore attractive targets for drug design, molecular engineering, and fundamental research on regulatory circuitry of living cells. Several mechanisms are known for riboswitches controlling gene expression, but most of them perform their roles by ligand binding. As with other macromolecules, knowledge of the 3D structure of riboswitches is crucial for the understanding of their function. The development of experimental methods allowed for investigation of RNA structure and its complexes with ligands (which are either riboswitches' substrates or inhibitors) and metal cations (which stabilize the structure and are also known to be riboswitches' inhibitors). The experimental probing of different states of riboswitches is however time consuming, costly, and difficult to resolve without theoretical support. The natural consequence is the use of computational methods at least for initial research, such as the prediction of putative binding sites of ligands or metal ions. Here, we present a review on such methods, with a special focus on knowledge-based methods developed in our laboratory: LigandRNA--a scoring function for the prediction of RNA-small molecule interactions and MetalionRNA--a predictor of metal ions-binding sites in RNA structures. Both programs are available free of charge as a Web servers, LigandRNA at http://ligandrna.genesilico.pl and MetalionRNA at http://metalionrna.genesilico.pl/.

In the recent years, it has become clear that a wide range of regulatory functions in bacteria are performed by riboswitches--regions of mRNA that change their structure upon external stimuli. Riboswitches are therefore attractive targets for drug design, molecular engineering, and fundamental research on regulatory circuitry of living cells. Several mechanisms are known for riboswitches controlling gene expression, but most of them perform their roles by ligand binding. As with other macromolecules, knowledge of the 3D structure of riboswitches is crucial for the understanding of their function. The development of experimental methods allowed for investigation of RNA structure and its complexes with ligands (which are either riboswitches' substrates or inhibitors) and metal cations (which stabilize the structure and are also known to be riboswitches' inhibitors). The experimental probing of different states of riboswitches is however time consuming, costly, and difficult to resolve without theoretical support. The natural consequence is the use of computational methods at least for initial research, such as the prediction of putative binding sites of ligands or metal ions. Here, we present a review on such methods, with a special focus on knowledge-based methods developed in our laboratory: LigandRNA--a scoring function for the prediction of RNA-small molecule interactions and MetalionRNA--a predictor of metal ions-binding sites in RNA structures. Both programs are available free of charge as a Web servers, LigandRNA at http://ligandrna.genesilico.pl and MetalionRNA at http://metalionrna.genesilico.pl/.

Phenomenologically important quantum dissipative processes include black-body friction (an atom absorbs counterpropagating blue-shifted photons and spontaneously emits them in all directions, losing kinetic energy) and non-contact van der Waals friction (in the vicinity of a dielectric surface, the mirror charges of the constituent particles inside the surface experience drag, slowing the atom). The theoretical predictions for these processes are modified upon a rigorous quantum electrodynamic (QED) treatment, which shows that the one-loop "correction" yields the dominant contribution to the off-resonant, gauge-invariant, imaginary part of the atom's polarizability at room temperature, for typical atom-surface interactions. The tree-level contribution to the polarizability dominates at high temperature., 5 pages; RevTeX

The attractive branch of the interaction potentials with the surface of gold have been computed for a large variety of atomic systems: the hydrogen atom, noble gases (He, Ne, Ar, Kr, Xe), alkali atoms (Li, Na, K, Rb, Cs) and alkaline atoms (Be, Mg, Ca, Sr, Ba). The results include highly accurate dynamic polarizabilities for the helium atom calculated using a variational method and explicitly correlated wavefunctions. For other atoms considered we used the data available in the literature. The interaction potentials include both the effects of retardation of the electromagnetic interactions and a realistic representation of the optical response function of gold (beyond the approximation of a perfect conductor). An explicit comparison of our result to the interaction between an atom and a perfect conductor is given., 8 pages, 1 figure

The thermal friction force acting on an atom moving relative to a thermal photon bath is known to be proportional to an integral over the imaginary part of the frequency-dependent atomic (dipole) polarizability. Using a numerical approach, we find that blackbody friction on atoms either in dilute environments or in hot ovens is larger than previously thought by orders of magnitude. This enhancement is due to far off-resonant driving of transitions by low-frequency thermal radiation. At typical temperatures, the blackbody radiation maximum lies far below the atomic transition wavelengths. Surprisingly, due to the finite lifetime of atomic levels, which gives rise to Lorentzian line profiles, far off-resonant excitation leads to the dominant contribution to the blackbody friction., 4 pages; RevTeX

In this chapter we review past and current experimental approaches to measuring the long-range interaction between atoms and surfaces, the so-called Casimir-Polder force. These experiments demonstrate the importance of going beyond the perfect conductor approximation and stipulate the relevance of the Dzyaloshinskii-Lifshitz-Pitaevskii theory. We discuss recent generalizations of that theory, that include higher multipole polarizabilities, and present a list of additional effects, that may become important in future Casimir-Polder experiments. Among the latter, we see great potential for spectroscopic techniques, atom interferometry, and the manipulation of ultra-cold quantum matter (e.g. BEC) near surfaces. We address approaches based on quantum reflection and discuss the atomic beam spin-echo experiment as a particular example. Finally, some of the advantages of Casimir-Polder techniques in comparison to Casimir force measurements between macroscopic bodies are presented.

The study was designed to demonstrate the relationship between the activity of human normal monocytes and blood platelets, to determine the metabolic activity of normal monocytes and monocytes cooperating with blood platelets in respect of their generation of reactive oxygen species (ROS) and to study the response of cooperating cells to nicotinamide (NA), 1-methylnicotinamide (MNA+) and 1-methyl-N'-hydroxymethylnicotinamide (MNAF+). The ability of those potential antiinflammatory compounds to inhibit oxygen respiratory burst was also assessed. Measurements were carried out by luminol chemiluminometry. The results of the measurements were compared to the data acquired for aspirin (ASA). The results obtained showed that MNAF inhibited oxygen burst in monocytes cooperating with platelets, whereas the two other compounds, NA and MNA, did not cause inhibition of oxygen burst in vitro at a statistically significant level.

We address some practically important and experimentally relevant questions concerning atom-surface interactions. For example, the quadrupole interaction of an atom with a dielectric macroscopic surface is obtained with full allowance for retardation and in closed form, valid for an arbitrary atom-surface distance. We also explore the relevance of higher-order multipole effects in atom-surface interactions, and we find that details in the dielectric response function of the surface material have to be resolved in order to accurately calculate the atom-surface potential. They lead to important effects at an intermediate range which cannot be explained by either short-range or long-range asymptotics. A numerical example (helium interacting with $\ensuremath{\alpha}$-quartz) is included in order to illustrate this aspect.

The helium pair potential was computed including relativistic and quantum electrodynamics contributions as well as improved accuracy adiabatic ones. Accurate asymptotic expansions were used for large distances R. Error estimates show that the present potential is more accurate than any published to date. The computed dissociation energy and the average R for the (4)He(2) bound state are 1.62+/-0.03 mK and 47.1+/-0.5 A. These values can be compared with the measured ones: 1.1(-0.2)(+0.3) mK and 52+/-4 A [R. E. Grisenti, Phys. Rev. Lett. 85, 2284 (2000)].

The complete ${\ensuremath{\alpha}}^{3}$ QED correction to the helium atom polarizability is computed assuming an infinite nuclear mass and found to be equal to 0.000 030 666(3) a.u., with the contribution from the electric-field dependence of the Bethe logarithm amounting to 0.000 000 193(2) a.u. After including the ${\ensuremath{\alpha}}^{2}$ and ${\ensuremath{\alpha}}^{3}$ corrections for the nuclear recoil and the leading part of the ${\ensuremath{\alpha}}^{4}$ QED correction, we find that the molar polarizability of $^{4}\mathrm{He}$ is $0.517\text{ }254\text{ }19(9)(4)\text{ }\text{ }{\mathrm{cm}}^{3}/\mathrm{mol}$. The first of the two error bounds is dominated by the uncertainty of ${\ensuremath{\alpha}}^{4}$ and higher-order QED corrections and the second reflects the uncertainty of the Avogadro constant.

The theory of long-range relativistic interactions in the Cowan-Griffin approximation is formulated and the expression for the leading-order relativistic correction to the dispersion energy is derived. It is shown that the relativistic dispersion energy for closed-shell atoms behaves as ${C}_{6}^{\mathrm{rel}}{R}^{\ensuremath{-}6}$ with the interatomic distance R. The relativistic correction to the van der Waals constant $\ensuremath{\delta}{C}_{6}$ is expressed as a Casimir-Polder integral of the product of a nonrelativistic frequency-dependent linear-response function with two dipole operators and a frequency-dependent quadratic-response function, including in addition one relativistic operator. In the Cowan-Griffin approximation, there are two contributions, involving the mass-velocity and the one-electron Darwin operators. The QED retardation effect on the long-range relativistic dispersion energy is also considered, and applications to the helium, calcium, and cadmium dimers are presented.

Nonrelativistically forbidden, single-photon transition rates between low lying states of the helium atom are rigorously derived within quantum electrodynamics theory. Equivalence of velocity and length gauges, including relativistic corrections is explicitly demonstrated. Numerical calculations of matrix elements are performed with the use of high precision variational wave functions and compared to former results., Comment: 11 pages, 1 figure, submitted to Phys. Rev. A