A simple and effective Verlet-type algorithm for simulating Langevin dynamics

We present a revision to the well known Störmer–Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate that the new algorithm correctly reproduces diffusive behaviour of a particle in a flat potential. For a harmonic oscillator, our algorithm provides the exact Boltzmann distribution for any value of damping, frequency and time step for both underdamped and overdamped behaviour within the usual stability limit of the Verlet algorithm. Given the structure and simplicity of the method, we conclude that this approach can trivially be adapted for contemporary applications, including molecular dynamics with extensions such as molecular constraints.     

Equivalent dose distribution analysis of Holocene eolian and fluvial quartz sands from Central Oklahoma

Holocene quartz sands were collected from fluvial terrace deposits and eolian dune deposits adjacent to the North Canadian and Cimarron Rivers and their tributaries in Central Oklahoma. Single aliquot regenerative dose optically stimulated luminescence techniques were employed to generate equivalent dose (ED) distribution histograms for each sample. We hypothesize that the ED distributions are convolutions of the distribution arising from natural sedimentary processes, influenced primarily by the degree of solar resetting experienced by individual grains, and a distribution due to experimental error. An estimation of the experimental error distribution for each sample was made and this was then deconvolved from the experimentally measured ED distribution to reveal the ‘sedimentary process’ ED distribution. Objective methods for determining EDs, uncertainties, and confidence parameters from the deconvolved distributions are presented.     

Morita Base Change in Hopf-Cyclic (Co)Homology

In this paper, we establish the invariance of cyclic (co)homology of left Hopf algebroids under the change of Morita equivalent base algebras. The classical result on Morita invariance for cyclic homology of associative algebras appears as a special example of this theory. In our main application we consider the Morita equivalence between the algebra of complex-valued smooth functions on the classical 2-torus and the coordinate algebra of the noncommutative 2-torus with rational parameter. We then construct a Morita base change left Hopf algebroid over this noncommutative 2-torus and show that its cyclic (co)homology can be computed by means of the homology of the Lie algebroid of vector fields on the classical 2-torus.     

The Prins Reaction in the Fragrance Industry: 100th Anniversary (1919–2019)

The Prins reaction, an acid‐catalyzed condensation of alkenes with aldehydes, is used extensively in the fragrance industry. This year we celebrate the 100th anniversary of the discovery of this reaction. In honor of this occasion we present an overview of the diverse applications of the Prins reaction in the synthesis of flavor and fragrance ingredients. To pay tribute to the inventor of the Prins reaction, Hendrik Jacobus Prins, we also provide some insight into his life, scientific, and entrepreneurial accomplishments.     

Contact resistance of quantum tubes

We consider the conductance of a quantum tube connected to a metallic contact. The number of angular momentum states that the tube can support depends on the strength of the radial confinement. We calculate the transmission coefficients which yield the conductance via the Landauer formula, and discuss the relation of our results to armchair carbon nanotubes embedded in a metal. For Al and Au contacts and tubes with a realistic radial confinement we find that the transmission can be close to unity corresponding to a contact resistance close to h / 2 e²per band at the Fermi level in the carbon nanotube.     

Polybismuthide Anions as Ligands: The Homoleptic Complex [(Bi7)Cd(Bi7)]4− and the Ternary Cluster [(Bi6)Zn3(TlBi5)]4−

We present the results from a reactivity study of the binary anion (TlBi₃)^2? towards Group 12 metal compounds MPh₂ (M=Zn, Cd, Hg) to gain access to coordination compounds of polycyclic polypnictide molecules such as Bi₇^3? or Bi₁₁^3?. The coordination chemistry of these polybismuthide cages has been unprecedented to date, while it has been known for a long time for the lighter Group 15 anions Pn₇^3? (Pn=P, As, Sb). The use of (TlBi₃)^2?, previously shown to release Tl under certain conditions in situ, resulted in the formation of the first heterometallic polyanion in which a nortricyclane‐type polybismuthide coordinates a transition‐metal atom, [(Bi₇)Cd(Bi₇)]^4?. Reactions with the lighter Group 12 metal precursor yielded the uncommon ternary cluster [(Bi₆)Zn₃(TlBi₅)]^4?, most likely representing a reaction intermediate, and at the same time hinting at the formation of the nortricyclane‐shaped cage. Quantum‐chemical studies provide deeper insight into the stability trends of the [(E₇)M(E₇)]^4? anion family and reveal a complex bonding situation in [(Bi₆)Zn₃(TlBi₅)]^4?, which features both localized and multi‐center bonding.     

A Photoswitchable Agonist for the Histamine H3 Receptor,a Prototypic Family A G‐Protein‐Coupled Receptor

Spatiotemporal control over biochemical signaling processes involving G protein‐coupled receptors (GPCRs) is highly desired for dissecting their complex intracellular signaling. We developed sixteen photoswitchable ligands for the human histamine H₃ receptor (hH₃R). Upon illumination, key compound 65 decreases its affinity for the hH₃R by 8.5‐fold and its potency in hH₃R‐mediated G_i protein activation by over 20‐fold, with the trans and cis isomer both acting as full agonist. In real‐time two‐electrode voltage clamp experiments in Xenopus oocytes, 65 shows rapid light‐induced modulation of hH₃R activity. Ligand 65 shows good binding selectivity amongst the histamine receptor subfamily and has good photolytic stability. In all, 65 (VUF15000) is the first photoswitchable GPCR agonist confirmed to be modulated through its affinity and potency upon photoswitching while maintaining its intrinsic activity, rendering it a new chemical biology tool for spatiotemporal control of GPCR activation.     

Shape morphing and topology optimization of fluid channels by explicit boundary tracking

An integrated shape morphing and topology optimization approach based on the deformable simplicial complex methodology is developed to address Stokes and Navier‐Stokes flow problems. The optimized geometry is interpreted by a set of piecewise linear curves embedded in a well‐formed triangular mesh, resulting in a physically well‐defined interface between fluid and impermeable regions. The shape evolution is realized by deforming the curves while maintaining a high‐quality mesh through adaption of the mesh near the structural boundary, rather than performing global remeshing. Topological changes are allowed through hole merging or splitting of islands. The finite element discretization used provides smooth and stable optimized boundaries for simple energy dissipation objectives. However, for more advanced problems, boundary oscillations are observed due to conflicts between the objective function and the minimum length scale imposed by the meshing algorithm. A surface regularization scheme is introduced to circumvent this issue, which is specifically tailored for the deformable simplicial complex approach. In contrast to other filter‐based regularization techniques, the scheme does not introduce additional control variables, and at the same time, it is based on a rigorous sensitivity analysis. Several numerical examples are presented to demonstrate the applicability of the approach.     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.