Highly fluorescent guanosine mimics for folding and energy transfer studies

Guanosines with substituents at the 8-position can provide useful fluorescent probes that effectively mimic guanine residues even in highly demanding model systems such as polymorphic G-quadruplexes and duplex DNA. Here, we report the synthesis and photophysical properties of a small family of 8-substituted-2′-deoxyguanosines that have been incorporated into the human telomeric repeat sequence using phosphoramidite chemistry. These include 8-(2-pyridyl)-2′-deoxyguanosine (2PyG), 8-(2-phenylethenyl)-2′-deoxyguanosine (StG) and 8-[2-(pyrid-4-yl)-ethenyl]-2′-deoxyguanosine (4PVG). On DNA folding and stability, 8-substituted guanosines can exhibit context-dependent effects but were better tolerated by G-quadruplex and duplex structures than pyrimidine mismatches. In contrast to previously reported fluorescent guanine analogs, 8-substituted guanosines exhibit similar or even higher quantum yields upon their incorporation into nucleic acids (Φ = 0.02-0.45). We have used these highly emissive probes to quantify energy transfer efficiencies from unmodified DNA nucleobases to 8-substituted guanosines. The resulting DNA-to-probe energy transfer efficiencies (ηt) are highly structure selective, with ηt(duplex) < ηt(single-strand) < ηt(G-quadruplex). These trends were independent of the exact structural features and thermal stabilities of the G-quadruplexes or duplexes containing them. The combination of efficient energy transfer, high probe quantum yield, and high molar extinction coefficient of the DNA provides a highly sensitive and reliable readout of G-quadruplex formation even in highly diluted sample solutions of 0.25 n

Diffusion of a liquid nanoparticle on a disordered substrate

We perform molecular dynamic simulations of liquid nanoparticles deposited on a disordered substrate. The motion of the nanoparticle is characterised by a 'stick and roll' diffusive process. Long simulation times ($\simeq \mu s$), analysis of mean square displacements and stacking time distribution functions demonstrate that the nanoparticle undergoes a normal diffusion in spite of long sticking times. We propose a phenomenological model for the size and temperature dependence of the diffusion coefficient in which the activation energy scales as $N^{1/3}$.Comment: Accepted for publication in Phys. Rev.

Inverse estimation of the transfer velocity of money

Monitoring the money supply is an important prerequisite for conducting sound monetary policy, yet monetary indicators are conventionally estimated in aggregate. This paper proposes a new methodology that is able to leverage micro-level transaction data from real-world payment systems. We apply a novel computational technique to measure the durations for which money is held in individual accounts, and compute the transfer velocity of money from its inverse. Our new definition reduces to existing definitions under conventional assumptions. However, inverse estimation remains suitable for payment systems where the total balance fluctuates and spending patterns change in time. Our method is applied to study Sarafu, a small digital community currency in Kenya, where transaction data is available from 25 January 2020 to 15 June 2021. We find that the transfer velocity of Sarafu was higher than it would seem, in aggregate, because not all units of Sarafu remained in active circulation. Moreover, inverse estimation reveals strong heterogineities and enables comparisons across subgroups of spenders. Some units of Sarafu were held for minutes, others for months, and spending patterns differed across communities using Sarafu. The rate of circulation and the effective balance of Sarafu changed substantially over time, as these communities experienced economic disruptions related to the COVID-19 pandemic and seasonal food insecurity. These findings contribute to a growing body of literature documenting the heterogeneous patterns underlying headline macroeconomic indicators and their relevance for policy. Inverse estimation may be especially useful in studying the response of spenders to targeted monetary operations

Liquid-liquid phase transition in Stillinger-Weber silicon

It was recently demonstrated that the Stillinger-Weber silicon undergoes a liquid-liquid first-order phase transition deep into the supercooled region (Sastry and Angell, Nature Materials 2, 739 (2003)). Here we study the effects of perturbations on this phase transition. We show that the order of the liquid-liquid transition changes with negative pressure. We also find that the liquid-liquid transition disappears when the three-body term of the potential is strengthened by as little as 5 %. This implies that the details of the potential could affect strongly the nature and even the existence of the liquid-liquid phase.Comment: 13 page

Toxicity of Ammonia and Nitrite to Aquatic Macroinvertebrates

The acute toxicity of ammonia was studied for six aquatic macroinvertebrate species (mayfly, stonefly, and caddisfly families). Two partial-chronic (24- and 30-day) tests were conducted on Pteronarcella badia. The acute toxicity of nitrite was studied for seven species, including one Diptera species; the mitigating effect of chloride ion on nitrite toxicity to two species was also investigated. For 6 tests on ammonia the median lethal concentration (96-hour LC50) values ranged from 1.8 to 5.0 mg/L un-ionized ammonia (NH3); in 19 tests less than 50% of the larvae died at the highest test concentration, so an LC50 could not be calculated. In the partial-chronic tests on P. badia, food consumption was not affected at concentrations up to 6.9 mg/L NH3, but concentrations in excess of 3.4 mg/L NH3 adversely affected nymphal survival rates and emergence of adults. For nitrite toxicity, test results showed a wide range of tolerance. The 96-hour LC50 for the single species of Diptera exceeded 123 mg/liter NO2-N; the 96-hour LC50 range for the other tests was between 0.25 and 2.4 mg/liter NO2-N. The addition of 10 mg/liter chloride ion in nitrite tests on P. badia and Ephemerella grandis resulted in a 3- to 10-fold decrease in 96-hour LC50 values. The tolerance to ammonia of the most sensitive of the insect species tested was greater than that reported in the literature for most species of fishes. Except for A. variegata, the range of acute toxicity of nitrite to the insects tested was similar to that reported for fishes

Nonmonotonic dependence of the absolute entropy on temperature in supercooled Stillinger-Weber silicon

Using a recently developed thermodynamic integration method, we compute the precise values of the excess Gibbs free energy (G^e) of the high density liquid (HDL) phase with respect to the crystalline phase at different temperatures (T) in the supercooled region of the Stillinger-Weber (SW) silicon [F. H. Stillinger and T. A. Weber, Phys. Rev. B. 32, 5262 (1985)]. Based on the slope of G^e with respect to T, we find that the absolute entropy of the HDL phase increases as its enthalpy changes from the equilibrium value at T \ge 1065 K to the value corresponding to a non-equilibrium state at 1060 K. We find that the volume distribution in the equilibrium HDL phases become progressively broader as the temperature is reduced to 1060 K, exhibiting van-der-Waals (VDW) loop in the pressure-volume curves. Our results provides insight into the thermodynamic cause of the transition from the HDL phase to the low density phases in SW silicon, observed in earlier studies near 1060 K at zero pressure.Comment: This version is accepted for publication in Journal of Statistical Physics (11 figures, 1 table

Properties of a continuous-random-network model for amorphous systems

We use a Monte Carlo bond-switching method to study systematically the thermodynamic properties of a "continuous random network" model, the canonical model for such amorphous systems as a-Si and a-SiO$_2$. Simulations show first-order "melting" into an amorphous state, and clear evidence for a glass transition in the supercooled liquid. The random-network model is also extended to study heterogeneous structures, such as the interface between amorphous and crystalline Si.Comment: Revtex file with 4 figure

Event-based relaxation of continuous disordered systems

A computational approach is presented to obtain energy-minimized structures in glassy materials. This approach, the activation-relaxation technique (ART), achieves its efficiency by focusing on significant changes in the microscopic structure (events). The application of ART is illustrated with two examples: the structure of amorphous silicon, and the structure of Ni80P20, a metallic glass.Comment: 4 pages, revtex, epsf.sty, 3 figure

Modelling of amorphous polymer surfaces in computer simulation

We study surface effects in amorphous polymer systems by means of computer simulation. In the framework of molecular dynamics, we present two different methods to prepare such surfaces. {\em Free} surfaces are stabilized solely by van--der--Waals interactions whereas {\em confined} surfaces emerge in the presence of repelling plates. The two models are compared in various computer simulations. For free surfaces, we analyze the migration of end--monomers to the surface. The buildup of density and pressure profiles from zero to their bulk values depends on the surface preparation method. In the case of confined surfaces, we find density and pressure oszillations next to the repelling plates. We investigate the influence of surfaces on the coordination number, on the orientation of single bonds, and on polymer end--to--end vectors. Furthermore, different statistical methods to determine location and width of the surface region for systems of various chain lengths are discussed and applied. We introduce a ``height function'' and show that this method allows to determine average surface profiles only by scanning the outermost layer of monomers.Comment: 23 pages, 12 figure

Nanojets, Electrospray, and Ion Field Evaporation: Molecular Dynamics Simulations and Laboratory Experiments

The energetics, interfacial properties, instabilities, and fragmentation patterns of electrosprays made from formamide salt solutions are investigated in a mass spectrometric vacuum electrospray experiment and using molecular dynamics (MD) simulations. The electrospray source is operated in a Taylor cone-jet mode, with the nanojet that forms being characterized by high surface-normal electric field strengths in the vicinity of 1 V/nm. Mass-to-charge ratios were determined for both positive and negative currents sprayed from NaI−formamide solutions with solute−solvent mole ratios of 1:8.4 and 1:36.9, and from KI−formamide solutions with mole ratios of 1:41 and 1:83. The molecular dynamics simulations were conducted on isolated 10 nm NaI−formamide droplets at mole ratios of 1:8 and 1:16. The droplet was subjected to a uniform electric field with strengths ranging between 0.5 and 1.5 V/nm. Both the experiments and simulations demonstrate a mixed charge emission regime where field-induced desorption of solvated ions and charged droplets occurs. The macroscopic parameters, such as average mass-to-charge ratio and maximum surface-normal field strengths deduced from the simulations are found to be in good agreement with the experimental work and consistent with electrohydrodynamic theory of cone-jets. The observed mass spectrometric Na+ and I− solvated ion distributions are consistent with a thermal evaporation process, and are correctly reproduced by the simulation after incorporation of the different flight times and unimolecular ion dissociation rates in the analysis. Alignment of formamide dipoles and field-induced reorganization of the positive and negative ionic charges in the interfacial region are both found to contribute to the surface-normal field near the points of charge emission. In the simulations the majority of cluster ions are found to be emitted from the tip of the jet rather than from the neck region next to the Taylor cone. This finding is consistent with the experimental energy distributions of the solvated ions which demonstrate that indeed most ions are emitted closer to the jet region, that is, beyond the cone-neck region where ohmic losses occur. This observation is also consistent with continuum electrohydrodynamic predictions of cluster-ion evaporation at surface regions of high curvature and therefore maximum surface electric field strengths, which may be the cone-neck region, the breakup region of the jet (usually near the tip of the jet), or the emitted charged droplets. In the nanoscale jets observed in this study, the regions of highest spatial curvature are at the ends of the jets where nascent drops either are forming or have just detached