Communication: Shifted forces in molecular dynamics

Simulations involving the Lennard-Jones potential usually employ a cutoff at r = 2.5σ. This communication investigates the possibility of reducing the cutoff. Two different cutoff implementations are compared, the standard shifted potential cutoff and the less commonly used shifted forces cutoff. The first has correct forces below the cutoff, whereas the shifted forces cutoff modifies Newton's equations at all distances. The latter is nevertheless superior; we find that for most purposes realistic simulations may be obtained using a shifted forces cutoff at r = 1.5σ, even though the pair force is here 30 times larger than at r = 2.5σ.     

A statistical approach to inelastic electron tunneling spectroscopy on fullerene-terminated molecules

We report on the vibrational fingerprint of single C(60) terminated molecules in a mechanically controlled break junction (MCBJ) setup using a novel statistical approach manipulating the junction mechanically to address different molecular configurations and to monitor the corresponding vibrational modes. In the IETS spectra, the vibrations of the anchoring C(60) dominate the spectra; thus information on the unit anchored with C(60) to the electrodes is masked by the modes arising from the anchoring groups. However, we have identified the additional modes from the fluorene backbone optically.     

A Triptycene‐Based Approach to Solubilising Carbon Nanotubes and C60

We describe herein the synthesis of a triptycene‐based surfactant designed with the ability to solubilise single‐walled carbon nanotubes (SWNTs) and C₆₀ in water through non‐covalent interactions. Furthermore, an amphiphilic naphthalene‐based surfactant with the same ability to solubilise SWNTs and C₆₀ has also been prepared. The compounds synthesised were designed with either two ionic or non‐ionic tails to ensure a large number of supramolecular interactions with the solvent, thereby promoting strong solubilisation. The surfactants produced stable suspensions in which the SWNTs are dispersed and the surfactant/SWNT complexes formed are stable for more than one year. UV/Vis/NIR absorption spectroscopy, TEM and AFM were employed to probe the solubilisation properties of the dispersion of surfactants and SWNTs in water.     

Collecting all intermediates with an optimal scaling for the generalised-active-space coupled-cluster method with application to SbH

ABSTRACT

A string-based coupled-cluster method of general excitation rank, with optimal scaling and easy collection of all possible intermediates, which accounts for special relativity within the four-component framework is presented. The easy identification and collection of intermediates is achieved by extending the excitation-class formalism and introducing a contraction order for the operator indices. Initially, all possible contractions between the Hamiltonian and the intermediates with the cluster operator are found, stored and used for driving the algorithm, thereby defining an algorithm which allows for very complex state-selective, multi-reference, coupled-cluster calculations. The algorithm for solving the coupled-cluster equations can be used in both relativistic as well as non-relativistic calculations by appropriate restrictions in the excitation-class formalism. The capabilities of the new method are demonstrated in the application to the electronic ground state of the SbH molecule. In these calculations simulated multi-reference expansions with double, triple and quadruple excitations into the external space as well as the regular coupled-cluster hierarchy up to full quadruples excitations are compared.     

An efficient algorithm for solving nonlinear equations with a minimal number of trial vectors: applications to atomic-orbital based coupled-cluster theory

The conjugate residual with optimal trial vectors (CROP) algorithm is developed. In this algorithm, the optimal trial vectors of the iterations are used as basis vectors in the iterative subspace. For linear equations and nonlinear equations with a small-to-medium nonlinearity, the iterative subspace may be truncated to a three-dimensional subspace with no or little loss of convergence rate, and the norm of the residual decreases in each iteration. The efficiency of the algorithm is demonstrated by solving the equations of coupled-cluster theory with single and double excitations in the atomic orbital basis. By performing calculations on H(2)O with various bond lengths, the algorithm is tested for varying degrees of nonlinearity. In general, the CROP algorithm with a three-dimensional subspace exhibits fast and stable convergence and outperforms the standard direct inversion in iterative subspace method.     

Quadratic response functions in a second-order polarization propagator framework

The linear and quadratic response functions have been derived for an exact state, based on an exponential parametrization of the time evolution consisting of products of exponentials for orbital rotations and for higher-order excitations. Truncating the linear response function such that the response function itself and its pole structure is correct to second order in M?ller-Plesset perturbation theory, we arrive at the second-order polarization propagator approximation (SOPPA). Previous derivations of SOPPA have used the superoperator formalism, making the extension of SOPPA to quadratic and higher order response functions difficult. The derivation of the quadratic response function is described in detail, allowing molecular properties such as hyperpolarizabilities, two-photon cross sections, and excited-state properties to be calculated using the SOPPA model.     

Local Transient Unfolding of Native State PAI‐1 Associated with Serpin Metastability

The metastability of the native fold makes serpin (serine protease inhibitor) proteins prone to pathological conformational change, often by insertion of an extra β‐strand into the central β‐sheet A. How this insertion is made possible is a hitherto unresolved question. By the use of advanced hydrogen/deuterium‐exchange mass spectrometry (HDX‐MS) it is shown that the serpin plasminogen activator inhibitor 1 (PAI‐1) transiently unfolds under native condition, on a second‐to‐minute time scale. The unfolding regions comprise β‐strand 5A as well as the underlying hydrophobic core, including β‐strand 6B and parts of helices A, B, and C. Based thereon, a mechanism is proposed by which PAI‐1 makes transitions through progressively more unfolded states along the reaction coordinate to the inactive, so‐called latent form. Our results highlight the profound utility of HDX‐MS in detecting sparsely populated, transiently unfolded protein states.     

Observables in 3d gravity and geodesic algebras

The algebra of quantum geodesics obtained by quantizing the coordinates of the Teichmller spaces is the quantumso _q(m) algebra by Nelson and Regge. Presented at the 9th Colloquium “Quantum Groups and Integrable Systems”, Prague, 22–24 June 2000.