Recognition determinants in a T4 ← G4 mutant derived from a 5′-GCGTGGGCGT-3′ oligomer in a zinc finger 268–DNA complex.

The 5′-GCGTGGGCGT-3′ (T4) oligomer found in the zinc finger 268–DNA complex was mutated into the sequence 5′-GCGGGGGCGT-3′ (G4). A 3D model was constructed from the T4 sequence using an X-ray structure as a template. Molecular dynamics simulations were used to test the thermal stability of the model. A 500-ps trajectory was obtained for the fully charged complex in water using GROMOS87. The complex and the G4 sequence are found to have dynamically stationary behavior. Comparisons made with a previous T4 sequence molecular dynamics simulation show both systems have similar thermal stability. The structure of DNA appears to be maintained by its global interactions with the protein although the mutated site does not contribute with its full potential for binding. The protein structure shows some small differences compared to the T4 simulation. The simulation provided evidence for the role of a chloride ion interacting with the protein and helping in the recognition process. Received: 21 June 1999 / Accepted: 19 October 1999 / Published online: 14 March 2000     

A generalized Langevin dynamics approach to model solvent dynamics effects on proteins via a solvent-accessible surface. The carboxypeptidase A inhibitor protein as a model

A generalized Langevin dynamics (GLD) scheme is derived for (bio)macromolecules having internal structure, arbitrary shapes and a size larger than solvent molecules (i.e. proteins). The concept of solvent-accessible surface area (SASA) is used to incorporate solvent effects via external forces thereby avoiding its explicit molecular representation. A simulation algorithm is implemented in the GROMOS molecular dynamics (MD) program including random forces and memory effects, while solvation effects enter via derivatives of the surface area. The potato carboxypeptidase inhibitor (PCI), a small protein, is used to numerically test the approach. This molecule has N- and C-terminal tails whose structure and fluctuations are solvent dependent. A 1-ns MD trajectory was analyzed in depth. X-ray and NMR structures are used in conjunction with MD simulations with and without explicit solvent to gauge the quality of the results. All the analyses showed that the GLD simulation approached the results obtained for the MD simulation with explicit simple-point-charge-model water molecules. The SASAs of the polar atoms show a natural exposure towards the solvent direction. A FLS solvent simulation was completed in order to sense memory effects. The approach and results presented here could be of great value for developing alternatives to the use of explicit solvent molecules in the MD simulation of proteins, expanding its use and the time-scale explored. Received: 2 February 2000 / Revised: 12 March 2000 / Accepted: 26 May 2000 / Published online: 2 November 2000     

Parabolic scaling of tree-shaped constructal network

We investigate the multi-scale structure of a tree network obtained by constructal theory and we propose a new geometrical framework to quantify deviations from scale invariance observed in many fields of physics and life sciences. We compare a constructally deduced fluid distribution network and one based on an assumed fractal algorithm. We show that: (i) the fractal network offers lower performance than the constructal object, and (ii) the constructal object exhibits a parabolic scaling explained in the context of the entropic skins geometry based on a scale diffusion equation in the scale space. Constructal optimization is equivalent to an equipartition of scale entropy production over scale space in the context of entropic skins theory. The association of constructal theory with entropic skins theory promises a deterministic theory to explain and build optimal arborescent structures.     

Combinatoric enumeration of two-dimensional proper arrays

An n×mproper array is a two-dimensional rectangular array composed of directed cubes that obey certain constraints. Because of these constraints, the n×m proper arrays may be classified via a schema in which each n×m proper array is associated with a particular n×1 column. For a fixed n, the goal is to enumerate, modulo symmetry, all possible edge configurations associated with n×m proper arrays. By varying n, one constructs four combinatoric sequences, each of which enumerates a particular class of edge configurations. Convolution arguments and resultant calculations associate these sequences with cubic equations. These cubic equations allow one to predict M_n, the number of edge configurations, modulo symmetry, associated with n×m proper arrays.     

Kinetic study of 2‐furanaldehyde, 3‐furanaldehyde,and 5‐methyl‐2‐furanaldehyde reactions initiated by Cl atoms

Rate coefficients for the gas‐phase reactions of chlorine atoms with a series of furanaldehydes have been determined at 298 ± 2 K and atmospheric pressure (708.5 ± 0.1). The experiments were performed using the relative technique combined with solid‐phase microextraction (SPME) sampling and gas chromatography with flame ionization detection (GC‐FID). Rate constants were determined relative to the reaction of Cl with n‐nonane and 2‐ethylfuran. The absolute rate coefficients k (in units of 10^?10 cm³ molecule^?1 s^?1) obtained were 2.61 ± 0.27 for 2‐furaldehyde, 3.15 ± 0.27 for 3‐furaldehyde, and 4 ± 0.5 for 5‐methyl‐2‐furaldehyde. This study shows that the reactions of furanaldehydes and Cl are very fast with little influence of the position of the aldehyde group or the presence of other substituent on the reactivity. The results seem to indicate a mechanism involving two main reaction channels, addition of chlorine atom to the double bond of the aromatic ring, and the abstraction of the aldehydic hydrogen. Further product studies are necessary to determine the mechanism of these reactions in more detail. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 670–678, 2008     

A unified approach to global convergence of trust region methods for nonsmooth optimization

This paper investigates the global convergence of trust region (TR) methods for solving nonsmooth minimization problems. For a class of nonsmooth objective functions called regular functions, conditions are found on the TR local models that imply three fundamental convergence properties. These conditions are shown to be satisfied by appropriate forms of Fletcher's TR method for solving constrained optimization problems, Powell and Yuan's TR method for solving nonlinear fitting problems, Zhang, Kim and Lasdon's successive linear programming method for solving constrained problems, Duff, Nocedal and Reid's TR method for solving systems of nonlinear equations, and El Hallabi and Tapia's TR method for solving systems of nonlinear equations. Thus our results can be viewed as a unified convergence theory for TR methods for nonsmooth problems.Research supported by AFOSR 89-0363, DOE DEFG05-86ER25017 and ARO 9DAAL03-90-G-0093.Corresponding author.     

Model calculation of the intrinsic barrier for proton transfer in a carbon acid

The intrinsic energy barrier for proton transfer in a model carbon acid-base system, H₃O⁺ + CH₂ =CH₂, is calculated. The role of basis sets, correlation energy, and solvation are discussed. The results are analyzed within the context of the use of the Marcus equation to characterize proton-transfer kinetics.     

Electron hopping conductivity and vapor sensing properties of flexible network polymer films of metal nanoparticles

Films of monolayer protected Au clusters (MPCs) with mixed alkanethiolate and omega-carboxylate alkanethiolate monolayers, linked together in a network polymer by carboxylate-Cu2+-carboxylate bridges, exhibit electronic conductivities (sigma(EL)) that vary with both the numbers of methylene segments in the ligands and the bathing medium (N2, liquid or vapor). A chainlength-dependent swelling/contraction of the film's internal structure is shown to account for changes in sigma(EL). The linker chains appear to have sufficient flexibility to collapse and fold with varied degrees of film swelling or dryness. Conductivity is most influenced (exponentially dependent) by the chainlength of the nonlinker (alkanethiolate) ligands, a result consistent with electron tunneling through the alkanethiolate chains and nonbonded contacts between those chains on individual, adjacent MPCs. The sigma(EL) results concur with the behavior of UV-vis surface plasmon adsorption bands, which are enhanced for short nonlinker ligands and when the films are dry. The film conductivities respond to exposure to organic vapors, decreasing in electronic conductivity and increasing in mass (quartz crystal microgravimetry, QCM). In the presence of organic vapor, the flexible network of linked nanoparticles allows for a swelling-induced alteration in either length or chemical nature of electron tunneling pathways or both.     

Fractionation of cadmium in tobacco and cigarette smoke condensate using XANES and sequential leaching with ICP-MS/MS

Analytical and Bioanalytical Chemistry - Fractionation data for cadmium in tobacco products, as obtained by sequential leaching of cadmium species with ICP-MS/MS analysis, and separately by X-ray...