Nonadiabatic alignment of asymmetric top molecules: field-free alignment of iodobenzene

Nonadiabatic laser alignment of an asymmetric top molecule is studied using the combination of a quantum dynamical theory and time-resolved photofragment imaging experiments. In particular, the degree of alignment of iodobenzene, induced by an intense, linearly polarized picosecond laser pulse, is calculated and measured. Pronounced alignment is obtained under field-free conditions.     

LIGHT-DRIVEN MOVEMENTS IN THE SOLAR TRACKING LEAF OF Lupinus palaestinus Boiss. (Fabaceae)

Abstract— The palmatcly-compound leaf lamina of Lupinus palaestinus Boiss. tracks the sun by independent diaphototropic movements of its individual leaflets, operated by the appropriate flexing of their pulvinules. The lamina also exhibits two additional, light-dependent nastic movements, that can operate concurrently with the diaphototropic response: (1) a nyctinastic response to light/dark transitions bv which all the leaflets fold down simultaneously and at equal rates, and which is reversed by a photonastic response to dark/light transitions by which all the leaflets unfold into a co-planar configuration; (2) a photonastic upward folding ("cupping"), which all the leaflets exhibit simultaneously and at equal rates in response to high irradiance. thereby modulating their diaphototropic response to reduce light interception and evade over-exposure. Although the individual leaflets can sense all these tight-signals and respond to them independently, they do so simultaneously, so that the entire lamina responds in a co-ordinated manner, as a unit. The photoreceptors for the two nastic responses are localized in the individual pulvinules and may or may not be the same. The photoreceptors for the diaphototropic perception are localized in the proximal segment of the lamina of the individual leaflets, adjacent to but outside the pulvinule. The separation of the sites of perception for the tropic and nastic responses allows these responses to operate concurrently. The capacity of the diaphototropic response to occur concurrently with one or the other of the two nastic responses may be accounted for by its inductive nature.     

First-order model potential for optical dipole transitions: Application to the lithium isoelectronic sequence

We have constructed two first-order model potentials which were designed to yield dipole transition moments, and have applied them to the lithium isoelectronic sequence. The models contain two or three adjustable parameters, chosen so as to reproduce selected transition moment data on a single ion of the sequence. With negligible computational effort, they both yield other transition moments of high accuracy.     

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other Monte Carlo moves. Our method extends traditional configurational bias by deleting a repeating motif (monomer) from one end of the biopolymer and regrowing it at the opposite end using the standard Rosenbluth scheme. The method's sampling efficiency compared to local moves, pivot rotations, and standard configurational bias is assessed by parameters relating to translational, rotational, and internal degrees of freedom of the oligonucleosome. Our results show that the end-transfer method is superior in sampling every degree of freedom of the oligonucleosomes over other methods at high salt concentrations (weak electrostatics) but worse than the pivot rotations in terms of sampling internal and rotational sampling at low-to-moderate salt concentrations (strong electrostatics). Under all conditions investigated, however, the end-transfer method is several orders of magnitude more efficient than the standard configurational bias approach. This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially for the traditional configurational-bias method. Thus, the method we propose can significantly improve performance for global biomolecular applications, especially in condensed systems with weak nonbonded interactions and may be combined with local enhancements to improve local sampling.     

DNA polymerase beta catalysis: are different mechanisms possible?

DNA polymerases are crucial constituents of the complex cellular machinery for replicating and repairing DNA. Discerning mechanistic pathways of DNA polymerase on the atomic level is important for revealing the origin of fidelity discrimination. Mammalian DNA polymerase beta (pol beta), a small (39 kDa) member of the X-family, represents an excellent model system to investigate polymerase mechanisms. Here, we explore several feasible low-energy pathways of the nucleotide transfer reaction of pol beta for correct (according to Watson-Crick hydrogen bonding) G:C basepairing versus the incorrect G:G case within a consistent theoretical framework. We use mixed quantum mechanics/molecular mechanics (QM/MM) techniques in a constrained energy minimization protocol to effectively model not only the reactive core but also the influence of the rest of the enzymatic environment and explicit solvent on the reaction. The postulated pathways involve initial proton abstraction from the terminal DNA primer O3'H group, nucleophilic attack that extends the DNA primer chain, and elimination of pyrophosphate. In particular, we analyze several possible routes for the initial deprotonation step: (i) direct transfer to a phosphate oxygen O(Palpha) of the incoming nucleotide, (ii) direct transfer to an active site Asp group, and (iii) transfer to explicit water molecules. We find that the most probable initial step corresponds to step (iii), involving initial deprotonation to water, which is followed by proton migration to active site Asp residues, and finally to the leaving pyrophosphate group, with an activation energy of about 15 kcal/mol. We argue that initial deprotonation steps (i) and (ii) are less likely as they are at least 7 and 11 kcal/mol, respectively, higher in energy. Overall, the rate-determining step for both the correct and the incorrect nucleotide cases is the initial deprotonation in concert with nucleophilic attack at the phosphate center; however, the activation energy we obtain for the mismatched G:G case is 5 kcal/mol higher than that of the matched G:C complex, due to active site structural distortions. Taken together, our results support other reported mechanisms and help define a framework for interpreting nucleotide specificity differences across polymerase families, in terms of the concept of active site preorganization or the so-called "pre-chemistry avenue".     

Incomplete Relative Semi-Abelian Categories

We propose relative (to a distinguished class E of epimorphisms) versions of the so-called old and new style axioms for semi-abelian categories, and prove the equivalence of these two sets of axioms. The same results were obtained before under much stronger completeness/cocompleteness assumptions. One of obvious purposes of such a generalization is to include the trivial case of E being the class of all isomorphisms when the ground category is an arbitrary pointed category.     

Effect of protic ionic liquids (PILs) on the formation of non-ionic dodecyl poly(ethylene oxide) surfactant self-assembly structures and the effect of these surfactants on the nanostructure of PILs

The ability of a series of non-ionic dodecyl poly(ethylene oxide) surfactants to form micelles in a variety of protic ionic liquids (PILs) was investigated using small and wide angle X-ray scattering (SAXS/WAXS). The C(12)E(n) surfactants with n = 3-8 were examined in PILs which contained either an ethyl, diethyl, triethyl, butyl, pentyl, ethanol or pentanol-ammonium cation in conjunction with either a nitrate or formate anion. The ability of the PILs to support micelles of these surfactants was highly dependent on their liquid nanostructure. The PILs containing hydroxyl groups on the cations were not nanostructured and had very low surfactant solubility (<1 wt%). The highly nanostructured PILs with butylammonium or pentylammonium cations contain large non-polar domains, and had excellent surfactant solubility, but due to the greater hydrocarbon solubility they had insufficient drive from the "solvophobic effect" to enable micelle formation. The PILs of ethylammonium nitrate (EAN), propylammonium nitrate (PAN), diethylammonium formate (DEAF) and triethylammonium formate (TEAF) had smaller non-polar domains, and all supported micelle formation below 20 wt% surfactant. The critical micelle concentration (CMC) of surfactants in EAN were two orders of magnitude greater than in water. The minimum molecular areas of the poly(ethylene oxide) head groups at the air/ionic liquid interface, A(min), were significantly larger in EAN than in water. The SAXS patterns from the micelles present in EAN fitted well to ellipsoids, whereas the micelles present in PAN fitted well to spheres. The nanostructure of select PILs was also influenced by the presence of surfactants.     

On the Form of Subobjects in Semi-Abelian and Regular Protomodular Categories

Let Gls denote the category of (possibly large) ordered sets with Galois connections as morphisms between ordered sets. The aim of the present paper is to characterize semi-abelian and regular protomodular categories among all regular categories ?, via the form of subobjects of ?, i.e. the functor ? → Gls which assigns to each object X in ? the ordered set Sub(X) of subobjects of X, and carries a morphism f : X → Y to the induced Galois connection Sub(X) → Sub(Y) (where the left adjoint maps a subobject m of X to the regular image of fm, and the right adjoint is given by pulling back a subobject of Y along f). Such functor amounts to a Grothendieck bifibration over ?. The conditions which we use to characterize semi-abelian and regular protomodular categories can be stated as self-dual conditions on the bifibration corresponding to the form of subobjects. This development is closely related to the work of Grandis on “categorical foundations of homological and homotopical algebra”. In his work, forms appear as the so-called “transfer functors” which associate to an object the lattice of “normal subobjects” of an object, where “normal” is defined relative to an ideal of null morphism admitting kernels and cokernels.     

Local surface patterning by chitosan-stabilized gold nanoparticles using the direct mode of scanning electrochemical microscopy (SECM)

An approach for patterning surfaces with prepared nanoparticles is described. Chitosan-stabilized gold nanoparticles (Au/chitosan NPs) were locally deposited on stainless steel (StSt), indium tin oxide (ITO), and highly-ordered pyrolytic graphite (HOPG). Deposition was driven by local pH gradient formed between a surface and a scanning electrochemical microscopy tip set in the direct mode. The pH at the substrate was increased upon biasing the surface by negative potentials, which caused the reduction of water. As the pH on the surface exceeded that of $ {\mathrm{pK}}_{{\mathrm{chitosanH}}^{+}}\sim 6.3 $ deprotonation of the amino groups of chitosan caused the irreversible deposition of the chitosan/AuNPs. The effect of different parameters, such as tip–surface distance and time, on deposition was studied. While the potential duration showed no clear influence, smaller tip–substrate distance and more negative potentials applied to the surface caused larger deposits. The overpotential needed for the deposition of nanoparticles on HOPG was the highest while that for StSt was the lowest. On the former, the sluggish kinetics caused the deposition of ring-shaped structures while disk-shaped deposits were formed on the other surfaces.