Ab initio molecular dynamics study of collective excitations in liquid H2_2O and D2_2O: Effect of dispersion corrections

The collective dynamics in liquid water is an active research topic experimentally, theoretically and via simulations. Here, ab initio molecular dynamics simulations are reported in heavy and ordinary water at temperature 323.15 K, or 50$^\circ$C. The simulations in heavy water were performed both with and without dispersion corrections. We found that the dispersion correction (DFT-D3) changes the relaxation of density-density time correlation functions from a slow, typical of a supercooled state, to exponential decay behaviour of regular liquids. This implies an essential reduction of the melting point of ice in simulations with DFT-D3. Analysis of longitudinal (L) and transverse (T) current spectral functions allowed us to estimate the dispersions of acoustic and optic collective excitations and to observe the L-T mixing effect. The dispersion correction shifts the L and T optic (O) modes to lower frequencies and provides by almost thirty per cent smaller gap between the longest-wavelength LO and TO excitations, which can be a consequence of a larger effective high-frequency dielectric permittivity in simulations with dispersion corrections. Simulation in ordinary water with the dispersion correction results in frequencies of optic excitations higher than in D$_2$O, and in a long-wavelength LO-TO gap of 24 ps$^{-1}$ (127 cm$^{-1}$).Comment: 14 pages, 9 figure

Profiles of electrostatic potential across the water-vapor, ice-vapor and ice-water interfaces

Ice-water, water-vapor interfaces and ice surface are studied by molecular dynamics simulations with the SPC/E model of water molecules having the purpose to estimate the profiles of electrostatic potential across the interfaces. We have proposed a methodology for calculating the profiles of electrostatic potential based on a trial particle, which showed good agreement for the case of electrostatic potential profile of the water-vapor interface of TIP4P model calculated in another way. The measured profile of electrostatic potential for the pure ice-water interface decreases towards the liquid bulk region, which is in agreement with simulations of preferential direction of motion of Li$^{+}$ and F$^{-}$ solute ions at the liquid side of the ice-water interface. These results are discussed in connection with the Workman-Reynolds effect.Comment: 7 pages, 5 figure

Solvation force for long ranged wall-fluid potentials

The solvation force of a simple fluid confined between identical planar walls is studied in two model systems with short ranged fluid-fluid interactions and long ranged wall-fluid potentials decaying as $-Az^{-p}, z\to \infty$, for various values of $p$. Results for the Ising spins system are obtained in two dimensions at vanishing bulk magnetic field $h=0$ by means of the density-matrix renormalization-group method; results for the truncated Lennard-Jones (LJ) fluid are obtained within the nonlocal density functional theory. At low temperatures the solvation force $f_{solv}$ for the Ising film is repulsive and decays for large wall separations $L$ in the same fashion as the boundary field $f_{solv}\sim L^{-p}$, whereas for temperatures larger than the bulk critical temperature $f_{solv}$ is attractive and the asymptotic decay is $f_{solv}\sim L^{-(p+1)}$. For the LJ fluid system $f_{solv}$ is always repulsive away from the critical region and decays for large $L$ with the the same power law as the wall-fluid potential. We discuss the influence of the critical Casimir effect and of capillary condensation on the behaviour of the solvation force.Comment: 48 pages, 12 figure

Scientific Standards and the Regulation of Genetically Modified Insects

Experimental releases of genetically modified (GM) insects are reportedly being evaluated in various countries, including Brazil, the Cayman Islands (United Kingdom), France, Guatemala, India, Malaysia, Mexico, Panama, Philippines, Singapore, Thailand, the United States of America, and Vietnam. GM mosquitoes (Aedes aegypti) have already been released for field trials into inhabited areas in the Cayman Islands (2009–?), Malaysia (2010–2011), and Brazil (2011–2012). Here, we assess the regulatory process in the first three countries permitting releases (Malaysia, US, and the Cayman Islands) in terms of pre-release transparency and scientific quality. We find that, despite 14 US government–funded field trials over the last 9 years (on a moth pest of cotton), there has been no scientific publication of experimental data, and in only two instances have permit applications been published. The world's first environmental impact statement (EIS) on GM insects, produced by US authorities in 2008, is found to be scientifically deficient on the basis that (1) most consideration of environmental risk is too generic to be scientifically meaningful; (2) it relies on unpublished data to establish central scientific points; and (3) of the approximately 170 scientific publications cited, the endorsement of the majority of novel transgenic approaches is based on just two laboratory studies in only one of the four species covered by the document. We find that it is not possible to determine from documents publically available prior to the start of releases if obvious hazards of the particular GM mosquitoes released in Malaysia, the Cayman Islands, and Brazil received expert examination. Simple regulatory measures are proposed that would build public confidence and stimulate the independent experimental studies that environmental risk assessments require. Finally, a checklist is provided to assist the general public, journalists, and lawmakers in determining, from documents issued by regulators prior to the start of releases, whether permit approval is likely to have a scientifically high quality basi

Velocity autocorrelations across the molecular-atomic fluid transformation in hydrogen under pressure

Non-monotonous changes in velocity autocorrelations across the transformation from molecular to atomic fluid in hydrogen under pressure are studied by ab initio molecular dynamics simulations at the temperature 2500 K. We report diffusion coefficients in a wide range of densities from purely molecular fluid up to metallic atomic fluid phase. An analysis of contributions to the velocity autocorrelation functions from the motion of molecular centers-of-mass, rotational and intramolecular vibrational modes is performed, and a crossover in the vibrational density of intramolecular modes across the transition is discussed.Comment: 7 pages, 5 figure

A new procedure for microarray experiments to account for experimental noise and the uncertainty of probe response

Although microarrays are routine analysis tools in biomedical research, theystill yield noisy output that often requires experimental confirmation. Manystudies have aimed at optimizing probe design and statistical analysis totackle this problem. However, less emphasis has been placed on controlling thenoise inherent to the experimental approach. To address this problem, weinvestigate here a procedure that controls for such experimental variance andcombine it with an assessment of probe performance. Two custom arrays were usedto evaluate the procedure: one based on 25mer probes from an Affymetrix designand the other based on 60mer probes from an Agilent design. To assessexperimental variance, all probes were replicated ten times. To assess probeperformance, the probes were calibrated using a dilution series of targetmolecules and the signal response was fitted to an absorption model. We foundthat significant variance of the signal could be controlled by averaging acrossprobes and removing probes that are nonresponsive. Thus, a more reliable signalcould be obtained using our procedure than conventional approaches. We suggestthat once an array is properly calibrated, absolute quantification of signalsbecomes straight forward, alleviating the need for normalization and referencehybridizations.<br

A Revised Design for Microarray Experiments to Account for Experimental Noise and Uncertainty of Probe Response

Background Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. Results Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal response was fitted to an adsorption model. We found that significant variance of the signal could be controlled by averaging across probes and removing probes that are nonresponsive or poorly responsive in the calibration experiment. Taking this into account, one can obtain a more reliable signal with the added option of obtaining absolute rather than relative measurements. Conclusion The assessment of technical variance within the experiments, combined with the calibration of probes allows to remove poorly responding probes and yields more reliable signals for the remaining ones. Once an array is properly calibrated, absolute quantification of signals becomes straight forward, alleviating the need for normalization and reference hybridizations

Integrating Time Into Family Business Research: Using Random Coefficient Modeling to Examine Temporal Influences on Family Firm Ambidexterity

Organizational ambidexterity refers to a firm’s ability to pursue both exploitation and exploration orientations. Despite research that suggests ambidexterity is a critical phenomenon in family firms, few studies directly examine the role of ambidexterity over time in family business. This study examines how family firm ambidexterity changes over time as a result of temporal-, firm-, and industry-level factors. We find that family firm ambidexterity is stable over time, punctuated by dramatic changes. We also find that the level of innovation required to compete in an industry is a predictor of changes in exploration versus exploitation over time among family firms.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

In Vitro Recombination of Non-Homologous Genes Can Result in Gene Fusions that Confer a Switching Phenotype to Cells

Regulation of protein activity is central to the complexity of life. The ability to regulate protein activity through exogenously added molecules has biotechnological/biomedical applications and offers tools for basic science. Such regulation can be achieved by establishing a means to modulate the specific activity of the protein (i.e. allostery). An alternative strategy for intracellular regulation of protein activity is to control the amount of protein through effects on its production, accumulation, and degradation. We have previously demonstrated that the non-homologous recombination of the genes encoding maltose binding protein (MBP) and TEM1 β-lactamase (BLA) can result in fusion proteins in which β-lactamase enzyme activity is allosterically regulated by maltose. Here, through use of a two-tiered genetic selection scheme, we demonstrate that such recombination can result in genes that confer maltose-dependent resistance to β-lactam even though they do not encode allosteric enzymes. These ‘phenotypic switch’ genes encode fusion proteins whose accumulation is a result of a specific interaction with maltose. Phenotypic switches represent an important class of proteins for basic science and biotechnological applications in vivo