Coupled map models for chaos in extended systems

Coupled maps with conserved quantities are introduced as models for chaos in extended systems. The long-wavelength limit of a simple one-dimensional example is investigated in detail. A Langevin equation for this system is derived, and the applicability of the fluctuation-dissipation theorem is discussed. Several numerical experiments to investigate possible thermodynamic properties are described.     

Collisional fragmentation of Ar@C60

The fragmentation patterns resulting from collisions between (Ar@C₆₀)⁺ or (Ar@C₆₀)⁻ ions and H₂, He, CH₄, Ne, Ar and Kr target gases have been measured. The ion-source material Ar@C₆₀ was synthesized by heating C₆₀ under 3000 atm of argon gas, leading to a 10⁻³ concentration of endohedral fullerenes. The fragmentation spectra (charged molecules only) are dominated by positive ions both when positive or negative endohedrals break up. Endohedral fragment ions Ar@C_n⁺ (48n60) as well as all carbon fragments are observed. For collisions involving (Ar@C₆₀)⁻, ejection of the Ar atom together with two electrons, without permanently damaging the fullerene cage, is a prominent reaction channel, indicating that a ‘window' or a deformation in the form of e.g. a large hole, through which the argon atoms can exit, is opened during the collision.     

LeadScope: software for exploring large sets of screening data

Modern approaches to drug discovery have dramatically increased the speed and quantity of compounds that are made and tested for potential potency. The task of collecting, organizing, and assimilating this information is a major bottleneck in the discovery of new drugs. We have developed LeadScope a novel, interactive computer program for visualizing, browsing, and interpreting chemical and biological screening data that can assist pharmaceutical scientists in finding promising drug candidates. The software organizes the chemical data by structural features familiar to medicinal chemists. Graphs are used to summarize the data, and structural classes are highlighted that are statistically correlated with biological activity.     

Insight into the complex and dynamic process of activation of matrix metalloproteinases.

Matrix metalloproteinases (MMPs) are important hydrolytic enzymes with profound physiological and pathological functions in living organisms. MMPs are produced in their inactive zymogenic forms, which are subsequently proteolytically activated in an elaborate set of events. The propeptide in the zymogen blocks the active site, with a cysteine side-chain thiolate from this propeptide achieving coordination with the catalytically important zinc ion in the active site. Molecular dynamics simulations, ab initio calculations, and wet chemistry experiments presented herein argue for the critical importance of a protonation event at the coordinated thiolate as a prerequisite for the departure of the propeptide from the active site. Furthermore, a catalytically important glutamate is shown to coordinate transiently to the active-site zinc ion to "mask" the positive potential of the zinc ion and lower the energy barrier for dissociation of the protonated cysteine side chain from the zinc ion. In addition, a subtle conformational change by the propeptide is needed in the course of zymogen activation. These elaborate processes take place in concert in the activation process of MMPs, and the insight into these processes presented herein sheds light on a highly regulated physiological process with profound consequences for eukaryotic organisms.     

The active site of a zinc-dependent metalloproteinase influences the computed pK(a) of ligands coordinated to the catalytic zinc ion

TNF-alpha converting enzyme (TACE) is a multidomain, membrane-anchored protein that includes a Zn-dependent protease domain. It releases the soluble form of cytokine tumor necrosis factor-alpha (TNF-alpha) from its membrane-bound precursor. TACE is a metalloprotease containing a catalytic glutamic acid, Glu-406, and a Zn(2+) ion ligated to three imidazoles. The protonation states of the active site glutamic acid and inhibitors are important factors in understanding the potency of inhibitors with acidic zinc-ligating groups such as hydroxamic and carboxylic acids. Density functional methods were utilized to compute pK(a) values using a model of the catalytic site of TACE and to predict a concomitant mechanism of binding, consistent with lowering the pK(a) of the bound ligand and raising the pK(a) of the active site Glu-406. Weak acids, such as hydroxamic acids, bind in their neutral form and then transfer an acidic proton to Glu-406. Stronger acids, such as carboxylic acids, bind in their anionic form and require preprotonation of Glu-406. Similar binding events would be expected for other zinc-dependent proteases.     

The molecular structure of selenonyl fluoride,SeO2F2, and sulfuryl fluoride,SO2F2, as determined by gas-phase electron diffraction

The molecular structure of selenonyl fluoride (SeO₂F₂) and sulfuryl fluoride (SO₂F₂) has been studied by gas-phase electron diffraction. The geometries of both molecules are consistent with predictions of VSEPR (valence-shell electron-pair repulsion) theory. The results for the more important distance (r_a), bond angle, and r.m.s. amplitude (l) parameters with estimated uncertainties estimated at 2σ are for SeO₂F₂r(Se = 0) = 1.575 Å (0.002), r(Se-F) = 1.685 Å (0.002), ∠OSeO = 126.2° (0.5), ∠FSeF = 94.1° (0.5), l(Se = 0) = 0.0440 Å (0.0046), l(Se-F) = 0.0472 Å (0.0042), and for SO₂F₂r(S = 0) = 1.397 Å (0.002), r(S-F) = 1.530 Å (0.002), ∠OSO = 122.6° (1.2), ∠FSF = 96.7° (1.1), l(S = 0) = 0.0331 Å (0.0015), l(S-F) = 0.0393 Å (0.0018).     

High-efficiency wideband gyro-TWTs and gyro-BWOs with helically corrugated waveguides

We review the studies of gyrotron-type microwave devices whose electrodynamic system has the form of an oversized metal waveguide with a helically corrugated internal surface. For certain parameters, such a corrugation changes radically the waveguide dispersion ensuring an almost constant group velocity of the eigenmode for a small (close to zero) longitudinal wave number in a wide frequency band. The use of “helical” waveguides along with electron optical systems which form near-axis electron beams makes it possible to create high-efficiency amplifiers based on gyro-traveling-wave tubes (gyro-TWTs) with a wide instantaneous frequency band of amplification and gyro-backward-wave oscillators (gyro-BWOs) with continuous wideband tuning of the oscillation frequency. The studied devices are superior to the well-studied microwave sources of this type (gyroklystrons and gyrotrons) in frequency band, by more than an order of magnitude, and are not inferior to them in efficiency even for a wide spread of electron velocities. __________ Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Radiofizika, Vol. 50, No. 2, pp. 104–117, February 2007.