A simple network of nodes moving on the circle

Two simple Markov processes are examined, one in discrete and one in continuous time, arising from idealized versions of a transmission protocol for mobile networks. We consider two independent walkers moving with constant speed on the discrete or continuous circle, and changing directions at independent geometric (respectively, exponential) times. One of the walkers carries a message that wishes to travel as far and as fast as possible in the clockwise direction. The message stays with its current carrier unless the two walkers meet, the carrier is moving counter‐clockwise, and the other walker is moving clockwise. Then the message jumps to the other walker. Explicit expressions are derived for the long‐term average clockwise speed and number of jumps made of the message, via the solution of associated boundary value problems. The tradeoff between speed and cost (measured as the rate of jumps) is also examined.     

Resonances of CH2(a 1A1) and their roles in unimolecular and bimolecular reactions

Low-lying resonances of the CH2(a 1A1) system (J=0) in an accurate ab initio potential energy surface are studied using a filter-diagonalization method. The width of these resonances fluctuates by more than two orders of magnitude and on average increases with the energy. Analysis of the resonance states concludes that the unimolecular decay of the excited molecular system near the dissociation threshold is neither mode specific nor statistical state specific. This is apparently due to remnant regularity embedded in the largely chaotic classical phase space, as evidenced by periodic orbit analysis. As a result, the Rice-Ramsperger-Kassel-Marcus and statistical adiabatic channel models overestimate the average unimolecular decay rate. The implications of the resonances for the bimolecular C(1D)+H2 reaction are also discussed.     

A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils

Pmel17 is a multidomain protein involved in biosynthesis of melanin. This process is facilitated by the formation of Pmel17 amyloid fibrils that serve as a scaffold, important for pigment deposition in melanosomes. A specific luminal domain of human Pmel17, containing 10 tandem imperfect repeats, designated as repeat domain (RPT), forms amyloid fibrils in a pH-controlled mechanism in vitro and has been proposed to be essential for the formation of the fibrillar matrix. Currently, no three-dimensional structure has been resolved for the RPT domain of Pmel17. Here, we examine the structure of the RPT domain by performing sequence threading. The resulting model was subjected to energy minimization and validated through extensive molecular dynamics simulations. Structural analysis indicated that the RPT model exhibits several distinct properties of β-solenoid structures, which have been proposed to be polymerizing components of amyloid fibrils. The derived model is stabilized by an extensive network of hydrogen bonds generated by stacking of highly conserved polar residues of the RPT domain. Furthermore, the key role of invariant glutamate residues is proposed, supporting a pH-dependent mechanism for RPT domain assembly. Conclusively, our work attempts to provide structural insights into the RPT domain structure and to elucidate its contribution to Pmel17 amyloid fibril formation.     

Synthesis,crystal structures and spectroscopic studies of calcium(II) succinamate(-1) complexes

The reaction of succinamic acid (H₂sucm) with Ca(NO₃)₂·4H₂O yielded compounds [Ca(Hsucm)(NO₃)(H₂O)]_n (1) and [Ca(Hsucm)₂]_n (2). The succinamate(-1) ligand presents two new ligation modes and coordinates through the two carboxylato and the amide O-atoms, thus bridging three Ca^II ions which assemble into zig-zag 1D chains in 1 and 2D networks in 2. Intermolecular hydrogen bonding interactions in the crystal structures of 1 and 2 result in overall 3D framework structures. Both compounds have been characterized by IR and ¹H NMR spectroscopy, and their thermal decomposition was monitored by TG/DTG and DSC measurements. The structural comparison of 1 and 2 with known lanthanide(III) succinamate(-1) complexes reveals differences in the coordination mode of the ligand and in the coordination number of the metal ions; the biological relevance of these differences is discussed.     

The gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields

Outer membranes are a crucial component of Gram-negative bacteria, containing standard lipids in their inner leaflet, lipopolysaccharides (LPSs) in their outer leaflet, and transmembrane β-barrels known as outer membrane proteins (OMPs). OMPs regulate functions such as substrate transport and cell movement, while LPSs act as a protective barrier for bacteria and can cause toxic reactions in humans. However, the experimental study of outer membranes is challenging. Molecular dynamics simulations are often used for the computational study of membrane systems, but the preparation of complex, LPS-rich outer membranes is not straightforward. The Gram-Negative Outer Membrane Modeler (GNOMM) is an automated pipeline for preparing simulation systems of OMPs embedded in LPS-containing membranes in four different force fields. Given the physiological and clinical importance of outer membranes and their components, GNOMM can be a useful tool in the study of their structure, function, and implications in diseases. GNOMM is available at http://bioinformatics.biol.uoa.gr/GNOMM . © 2019 Wiley Periodicals, Inc.     

Excited‐State Dynamics of a Two‐Photon‐Activatable Ruthenium Prodrug

We present a new approach to investigate how the photodynamics of an octahedral ruthenium(II) complex activated through two‐photon absorption (TPA) differ from the equivalent complex activated through one‐photon absorption (OPA). We photoactivated a Ru^II polypyridyl complex containing bioactive monodentate ligands in the photodynamic therapy window (620–1000 nm) by using TPA and used transient UV/Vis absorption spectroscopy to elucidate its reaction pathways. Density functional calculations allowed us to identify the nature of the initially populated states and kinetic analysis recovers a photoactivation lifetime of approximately 100 ps. The dynamics displayed following TPA or OPA are identical, showing that TPA prodrug design may use knowledge gathered from the more numerous and easily conducted OPA studies.     

Proximal minimizations with D-functions and the massively parallel solution of linear network programs

This paper discusses the massively parallel solution of linear network programs. It integrates the general algorithmic framework of proximal minimization with D-functions (PMD) with primal-dual row-action algorithms. Three alternative algorithmic schemes are studied: quadratic proximal point, entropic proximal point, and least 2-norm perturbations. Each is solving a linear network problem by solving a sequence of nonlinear approximations. The nonlinear subproblems decompose for massively parallel computing. The three algorithms are implemented on a Connection Machine CM-2 with up to 32K processing elements, and problems with up to 16 million variables are solved. A comparison of the three algorithms establishes their relative efficiency. Numerical experiments also establish the best internal tactics which can be used when implementing proximal minimization algorithms. Finally, the new algorithms are compared with an implementation of the network simplex algorithm executing on a CRAY Y-MP vector supercomputer.     

Direct versus indirect H atom elimination from photoexcited phenol molecules

The active role of the optically dark pi sigma* state, following UV absorption, has been implicated in the photochemistry of a number of biomolecules. This work focuses on the role of the pi sigma* state in the photochemistry of phenol upon excitation at 200 nm. By probing the neutral hydrogen following UV excitation, we show that hydrogen elimination along the dissociative pi sigma* potential energy surface occurs within 103 +/- 30 fs, indicating efficient coupling at the S1/S2 and S0/S2 conical intersections, with no identifiable role of statistical unimolecular decay of vibronically excited (S0) phenol in the timeframe of our measurements.     

Investigation of multiple electronic excited state relaxation pathways following 200 nm photolysis of gas-phase imidazole

Imidazole acts as a subunit in the DNA base adenine and the amino acid histidine-both important biomolecules which display low fluorescence quantum yields following UV excitation. The low fluorescence quantum yields are attributed to competing non-radiative excited state relaxation pathways that operate on ultrafast timescales. Imidazole is investigated here as a model compound due to its accessibility to high level ab initio calculations and time-resolved gas-phase spectroscopic techniques. Recent non-adiabatic dynamics simulations have identified three non-radiative relaxation mechanisms which are active following 6.0-6.2 eV excitation. Presented herein is a comprehensive investigation of each mechanism using a combination of femtosecond time-resolved ion yield and total kinetic energy release spectroscopies to monitor the formation of associated photoproducts. Relaxation along the (1)πσ state constitutes the predominant deactivation pathway. Timescales for NH-dissociation are extracted and distinguished from alternative H-atom sources based on their kinetic energy distributions. Larger photoproducts are observed to a lesser extent and attributed to ring fragmentation following NH-puckering and CN-stretching relaxation paths.