Coupling for Markov renewal processes and the rate of convergence in ergodic theorems for processes with semi-Markov switchings

Coupling procedures for Markov renewal processes are described. Applications to ergodic theorems for processes with semi-Markov switchings are considered.This paper was partly prepared with the support of NFR Grant F-UP 10257-300.     

Topography of the free-energy landscape probed via mechanical unfolding of proteins

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)-fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.     

Reactions of carbamoylated amino enones with 3-substituted chromones for the preparation of 2-pyridones and chromeno[4,3-b]pyridine-2,5-diones

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Importance of van der Waals interaction for organic molecule-metal junctions: adsorption of thiophene on Cu(110) as a prototype

We report ab initio calculations for the interface energetics of a weakly adsorbed organic molecule on a metal surface, which serves as a model interface relevant for organic electronics. The studied thiophene ring is found to be physisorbed on the Cu(110) surface with an adsorption energy of -0.50 eV. Nonlocal correlations, i.e., van der Waals interactions, are solely responsible for the binding in this weakly interacting system, and the choice of the proper exchange-correlation function is crucially important. The adsorption of thiophene lowers the metal work function due to the formation of surface dipoles while no sizable charge transfer is found.     

A 19F NMR Study of the Transmissive Ability of Boron-Containing Bridged Systems with Three- and Four-Coordinated Boron Atoms

Two series of model compounds, Ar₂BOC₆H₄F-4 and Ar₂B(Py)OC₆H₄F-4, containing three-and four-coordinated boron atoms, have been synthesized. It was established by ¹⁹F NMR technique that both systems possess a similar transmissive ability that is in intermolecular coordination with pyridine does not influence the transmissive properties of the boron-oxygen binuclear bridging group. The solvent polarity does not influence the electron transmission in the boron complexes studied.     

Correction to: Accelerating Reactive Transport Modeling: On-Demand Machine Learning Algorithm for Chemical Equilibrium Calculations

Transport in Porous Media - In the original publication of the article, Table 2 was published incorrectly.     

Numerical solution of the problem of computational time reversal in a quadrant

The problem of computational time reversal is posed as the inverse problem of the determination of an unknown initial condition with a finite support in a hyperbolic equation, given the Cauchy data at the lateral surface. Two such two-dimensional inverse problems are solved numerically in the case when the domain is a quadrant and the Cauchy data are given at finite parts of the coordinate axes. The previously obtained Lipschitz stability estimate implies refocusing of the time-reversed wave field in the case of a small amount of noise in the data. It also indicates the possibility of good performance of a proper numerical method. Such performance is demonstrated in this paper for a particular problem and a particular numerical method.     

Superbase‐catalyzed domino 3H‐pyrroles synthesis from ketoximes and acetylene: DFT study vs experiment

Elimination of vinyl alcohol from 5‐vinyloxypyrrolines in the presence of superbases (final step of domino 3H‐pyrroles synthesis from ketoximes and acetylene) is studied computationally at different levels of theory in DMSO solution (PCM). The sequences of transformations starting from nucleophilic addition of hydroxide ion to carbon‐carbon or carbon‐nitrogen double bonds are proposed as possible mechanisms. Unusual reactivity of 2,5‐dimethylphenyl substituted 5‐vinyloxypyrroline is explained within these mechanisms.