Time-Reversal and Entropy

There is a relation between the irreversibility of thermodynamic processes as expressed by the breaking of time-reversal symmetry, and the entropy production in such processes. We explain on an elementary mathematical level the relations between entropy production, phase-space contraction and time-reversal starting from a deterministic dynamics. Both closed and open systems, in the transient and in the steady regime, are considered. The main result identifies under general conditions the statistical mechanical entropy production as the source term of time-reversal breaking in the path space measure for the evolution of reduced variables. This provides a general algorithm for computing the entropy production and to understand in a unified way a number of useful (in)equalities. We also discuss the Markov approximation. Important are a number of old theoretical ideas for connecting the microscopic dynamics with thermodynamic behavior.     

Relaxation of Alkali Glass Exposed to an Electron Beam

Binary potassium and rubidium silicate glasses were irradiated with high-energy electrons. The changes induced in the glasses were observed as a decay of alkali X-ray signals with time. The decay curves displayed incubation periods, connected with changes of the transport mechanism. The electron exposures were interrupted relative to the incubation periods, next the glasses were annealed to enable easier relaxations, and successively irradiated again to finish the decay curve. Relaxation, which depends on the point of the decay curve at which exposure is interrupted, is calculated for the glasses. Relaxation was found to depend strongly on the interruption point with regard to the incubation period. The longer irradiation causes worse recovery of the structure during annealing, especially if the irradiation lasts longer than the incubation time. The larger ions and lower concentration also inhibit relaxation.     

Nanobody‐Enabled Reverse Pharmacology on G‐Protein‐Coupled Receptors

The conformational complexity of transmembrane signaling of G‐protein‐coupled receptors (GPCRs) is a central hurdle for the design of screens for receptor agonists. In their basal states, GPCRs have lower affinities for agonists compared to their G‐protein‐bound active state conformations. Moreover, different agonists can stabilize distinct active receptor conformations and do not uniformly activate all cellular signaling pathways linked to a given receptor (agonist bias). Comparative fragment screens were performed on a β₂‐adrenoreceptor–nanobody fusion locked in its active‐state conformation by a G‐protein‐mimicking nanobody, and the same receptor in its basal‐state conformation. This simple biophysical assay allowed the identification and ranking of multiple novel agonists and permitted classification of the efficacy of each hit in agonist, antagonist, or inverse agonist categories, thereby opening doors to nanobody‐enabled reverse pharmacology.     

Analytic models for parameter dependency in option price modelling

Options are a type of financial instrument classed as derivatives, as they derive their value from an underlying asset. The equations used to model the option price are often expressed as partial differential equations (PDEs). Once expressed in this form, a discretization method on a finite grid can be applied and the numerical valuation obtained. Remains the problem of writing down an (approximate) closed-form analytic model for the option price in function of all the variables and parameters, which is the main objective of this paper. At the same time we also consider the Greeks, which are the quantities representing the sensitivities of the price to a change in the underlying variables or parameters. Discrete values for these Greeks can again be derived, either directly from the differentiation matrices occurring in the option price PDE or by solving new but similar PDEs. Next, analytic models for the Greeks are computed in the same way as for the option price. As a prototype case, The Black-Scholes PDE for European call options is considered.     

Analysis of explosives using differential mobility spectrometry

Characterization of ions from eight explosives (2,4,6-trinitrotoluene, pentaerythritol tetranitrate, 2,4,6-trinitrophenol, 2,4-dinitrotoluene, erythritol tetranitrate, hexamethylene triperoxide diamine, 2,4,6-trinitrophenylmethylnitramine and 1,3,5-trinitro-perhydro-1,3,5-triazine) using differential mobility spectrometry (DMS) with ⁶³Ni as an ionization source was performed. Presented results of explosive analysis have been evaluated by use of special software tool which communicates with DMS in real time. This tool was developed for visualization, identification and comparison of measured data. Each explosive provides characteristic signal at a specific compensation voltage under a fixed dispersion field. Peaks in DMS spectra for these ions were confined to a range of compensation voltages between ?1.61 to +1.71 V at RF = 1060 V. We calculated specific alpha coefficients (α₂ and α₄) to obtain a nonlinear function of explosives, based on their DMS spectra. Dependence of mobility for measured explosives ions in electric field at E/N values between 0 to 120 Td were used to inspectional graphical differentiation of explosives.     

X‐ray nanotomography and focused‐ion‐beam sectioning for quantitative three‐dimensional analysis of nanocomposites

Knowing the relationship between three‐dimensional structure and properties is paramount for complete understanding of material behavior. In this work, the internal nanostructure of micrometer‐size (～10 µm) composite Ni/Al particles was analyzed using two different approaches. The first technique, synchrotron‐based X‐ray nanotomography, is a nondestructive method that can attain resolutions of tens of nanometers. The second is a destructive technique with sub‐nanometer resolution utilizing scanning electron microscopy combined with an ion beam and `slice and view' analysis, where the sample is repeatedly milled and imaged. The obtained results suggest that both techniques allow for an accurate characterization of the larger‐scale structures, while differences exist in the characterization of the smallest features. Using the Monte Carlo method, the effective resolution of the X‐ray nanotomography technique was determined to be ～48 nm, while focused‐ion‐beam sectioning with `slice and view' analysis was ～5 nm.     

Molecular structure of guanine-quartet supramolecular assemblies in a gel-state based on a DFT calculation of infrared and vibrational circular dichroism spectra

The infrared (IR) and vibrational circular dichroism (VCD) spectra of guanosine-5'-hydrazide ( G-1), a powerful hydrogelator, have been measured and analyzed on the basis of ab initio modeling. B3LYP/6-31G** DFT calculations predict that G-1, forming a clear solution in deuterated DMSO, is present in monomeric form in this solvent, whereas strong gelation in a phosphate buffer is due to the formation of a guanine-quartet structure, ( G-1)4, in which the four G-1 are linked by hydrogen-bonded guanine moieties and stabilized by an alkali metal cation. The B3LYP/6-31G** IR and VCD spectra of the nearly planar G-quartet, whose structure is slightly distorted from the C4h symmetry, in which the G-bases interact via four Hoogsteen-type hydrogen bonds and a sodium cation is positioned in the middle of the G-quartet, are in very good agreement with the experimental spectra, indicating that this structure is the predominant structure in the gel state. The geometric parameters are discussed. This study is the first to use IR and VCD spectroscopies coupled with DFT calculations to elucidate the structure of a supramolecular species in a gel state and shows the VCD spectroscopy as a powerful method for investigating the structure of complex supramolecular self-assemblies where the use of other structural methods is limited.     

Aggregation behavior of nucleoside-boron cluster conjugates in aqueous solutions

We report the first evidence that boron-containing nucleoside conjugates have a tendency to associate in water solutions. The size, charge, and exoskeletal pattern of the boron cluster can strongly influence the aggregation. The aggregation of nucleosides with attached boron clusters was observed using light scattering and atomic force microscopy techniques. Although the species containing either the bulky amphiphilic [3-cobalt(III) bis(1,2-dicarbollide)]- anion or the electroneutral dicarba-closo-dodecaboranyl moiety tend to form stable nanoparticles in aqueous solutions, the compounds bearing the smaller, negatively charged dicarba-nido-undecaboranyl moiety as well as the unmodified nucleosides do not aggregate. The light scattering measurements also showed that the aggregated species can interact with nonionic surfactant Triton X-100 in solution. The partition coefficients P in the water-octanol system correlate fairly well with the aggregation tendency observed by light scattering measurements. This finding allows us to predict the association behavior of boron-cluster-containing nucleosides on a qualitative level. The observed phenomenon can contribute to a better understanding of biological properties of boronated nucleosides and the design of boronated nucleoside-based drugs such as boron carriers for boron neutron capture therapy of tumors (BNCT) and antiviral agents.     

Comparison of negative ion electrospray mass spectra measured by seven tandem mass analyzers towards library formation

A library of negative ion electrospray ionization mass spectra and tandem mass spectra (MS/MS) of sulfonated dyes has been developed for fast identification purposes. The uniform protocol has been elaborated and applied to the measurements of more than 50 anionic dyes. Three collision energies are selected in our protocol which ensures that at least one of them provides a suitable ratio of product ions to the precursor ion. The robustness is investigated with altered values of tuning parameters (e.g. the pressure of the nebulizing gas, the temperature and the flow rate of drying gas, and the mobile phase composition). The results of the inter-laboratory comparison of product ion mass spectra recorded on seven different tandem mass spectrometers (three ion traps, two triple quadrupoles and two hybrid quadrupole time of flight instruments) are presented for four representative anionic dyes--azo dye Acid Red 118, anthraquinone dye Acid Violet 43, triphenylmethane dye Acid Blue 1 and Al(III) metal-complex azo dye. The fragmentation patterns are almost identical for all tandem mass analyzers, only the ratios of product ions differ somewhat which confirms the possibility of spectra transfer among different mass analyzers with the goal of library formation.     

Preparation and characterization of self-assembled nanoparticles formed by poly(ethylene oxide)-block-poly(epsilon-caprolactone) copolymers with long poly(epsilon-caprolactone) blocks in aqueous solutions

Aqueous solutions of self-assembled nanoparticles formed by biocompatible diblock copolymers of poly(epsilon-caprolactone)-block-poly(ethylene oxide) (PCL-PEO) with the same molar mass of the PEO block (5000 g mol-1) and three different molar masses of the PCL block (5000, 13 000, and 32 000 g mol-1) have been prepared by a fast mixing the copolymer solution in a mild selective solvent, tetrahydrofuran (THF)/water, with an excess of water, that is, by quenching the reversible micellization equilibrium, and a subsequent removal of THF by dialysis of the water-rich solution against water. The prepared nanoparticles have been characterized by static and dynamic light scattering and atomic force microscopy imaging. It was found that stable monodisperse nanoparticles are formed only if the initial mixed solvent contained 90 vol % THF. The results show that the prepared nanoparticles are spherical vesicles with relatively thick hydrophobic walls, that is, spherical core/shell nanoparticles with the hollow core filled with the solvent.