Modeling the Construction of Polymeric Adsorbent Media: Effects of Counter-Ions on Ligand Immobilization and Pore Structure

Molecular dynamics modeling and simulations are employed to study the effects of counter-ions on the dynamic spatial density distribution and total loading of immobilized ligands as well as on the pore structure of the resultant ion exchange chromatography adsorbent media. The results show that the porous adsorbent media formed by polymeric chain molecules involve transport mechanisms and steric resistances which cause the charged ligands and counter-ions not to follow stoichiometric distributions so that (i) a gradient in the local nonelectroneutrality occurs, (ii) non-uniform spatial density distributions of immobilized ligands and counter-ions are formed, and (iii) clouds of counter-ions outside the porous structure could be formed. The magnitude of these counter-ion effects depends on several characteristics associated with the size, structure, and valence of the counter-ions. Small spherical counter-ions with large valence encounter the least resistance to enter a porous structure and their effects result in the formation of small gradients in the local nonelectroneutrality, higher ligand loadings, and more uniform spatial density distributions of immobilized ligands, while the formation of exterior counter-ion clouds by these types of counter-ions is minimized. Counter-ions with lower valence charges, significantly larger sizes, and elongated shapes, encounter substantially greater steric resistances in entering a porous structure and lead to the formation of larger gradients in the local nonelectroneutrality, lower ligand loadings, and less uniform spatial density distributions of immobilized ligands, as well as substantial in size exterior counter-ion clouds. The effects of lower counter-ion valence on pore structure, local nonelectroneutrality, spatial ligand density distribution, and exterior counter-ion cloud formation are further enhanced by the increased size and structure of the counter-ion. Thus, the design, construction, and functionality of polymeric porous adsorbent media will significantly depend, for a given desirable ligand to be immobilized and represent the adsorption active sites, on the type of counter-ion that is used during the ligand immobilization process. Therefore, the molecular dynamics modeling and simulation approach presented in this work could contribute positively by representing an engineering science methodology to the design and construction of polymeric porous adsorbent media which could provide high intraparticle mass transfer and adsorption rates for the adsorbate biomolecules of interest which are desired to be separated by an adsorption process

A Molecular Dynamics Study on the Transport of a Charged Biomolecule in a Polymeric Adsorbent Medium and Its Adsorption onto a Charged Ligand

The transport of a charged adsorbate biomolecule in a porous polymeric adsorbent medium and its adsorption onto the covalently immobilized ligands have been modeled and investigated using molecular dynamics modeling and simulations as the third part of a novel fundamental methodology developed for studying ion-exchange chromatography based bioseparations. To overcome computational challenges, a novel simulation approach is devised where appropriate atomistic and coarse grain models are employed simultaneously and the transport of the adsorbate is characterized through a number of locations representative of the progress of the transport process. The adsorbate biomolecule for the system studied in this work changes shape, orientation, and lateral position in order to proceed toward the site where adsorption occurs and exhibits decreased mass transport coefficients as it approaches closer to the immobilized ligand. Furthermore, because the ligands are surrounded by counterions carrying the same type of charge as the adsorbate biomolecule, it takes the biomolecule repeated attempts to approach toward a ligand in order to displace the counterions in the proximity of the ligand and to finally become adsorbed. The formed adsorbate-ligand complex interacts with the counterions and polymeric molecules and is found to evolve slowly and continuously from one-site (monovalent) interaction to multisite (multivalent) interactions. Such a transition of the nature of adsorption reduces the overall adsorption capacity of the ligands in the adsorbent medium and results in a type of surface exclusion effect. Also, the adsorption of the biomolecule also presents certain volume exclusion effects by not only directly reducing the pore volume and the availability of the ligands in the adjacent regions, but also causing the polymeric molecules to change to more compact structures that could further shield certain ligands from being accessible to subsequent adsorbate molecules. These findings have significant practical implications to the design and construction of polymeric porous adsorbent media for effective bioseparations and to the synthesis and operation of processes employed in the separation of biomolecules. The modeling and analysis methods presented in this work could also be suitable for the study of biocatalysis where an enzyme is immobilized on the surface of the pores of a porous medium

Path sampling for atmospheric reactions: Formic acid catalysed conversion of SO3 + H2O to H2SO4

Atmospheric reactions, hitherto studied computationally mainly with static computations in conjunction with transition state theories, can be further described via path sampling calculations. Here we report on an exploratory study of the formic acid catalysed hydrolysis of SO3 to produce H2SO4. We demonstrate that precise measurements of rate coefficients can be obtained in principle for such reactions with an acceptable expenditure of computational resources, and that new insights into the reaction can be obtained by the analysis of the path space explored via path sampling techniques.Peer reviewe

Local initiation conditions for water autoionization

The pH of liquid water is determined by the infrequent process in which water molecules split into short-lived hydroxide and hydronium ions. This reaction is difficult to probe experimentally and challenging to simulate. One of the open questions is whether the local water structure around a slightly stretched OH bond is actually initiating the eventual breakage of this bond or whether this event is driven by a global ordering that involves many water molecules far away from the reaction center. Here, we investigated the self-ionization of water at room temperature by rare-event ab initio molecular dynamics and obtained autoionization rates and activation energies in good agreement with experiments. Based on the analysis of thousands of molecular trajectories, we identified a couple of local order parameters and show that if a bond stretch occurs when all these parameters are around their ideal range, the chance for the first dissociation step (double-proton jump) increases from 10(-7) to 0.4. Understanding these initiation triggers might ultimately allow the steering of chemical reactions

Numerical control matrix rotation for the LINC-NIRVANA Multi-Conjugate Adaptive Optics system

LINC-NIRVANA will realize the interferometric imaging focal station of the Large Binocular Telescope. A double Layer Oriented multi-conjugate adaptive optics system assists the two arms of the interferometer, supplying high order wave-front correction. In order to counterbalance the field rotation, mechanical derotation for the two ground wave-front sensors, and optical derotators for the mid-high layers sensors fix the positions of the focal planes with respect to the pyramids aboard the wave-front sensors. The derotation introduces pupil images rotation on the wavefront sensors: the projection of the deformable mirrors on the sensor consequently change. The proper adjustment of the control matrix will be applied in real-time through numerical computation of the new matrix. In this paper we investigate the temporal and computational aspects related to the pupils rotation, explicitly computing the wave-front errors that may be generated.Comment: 6 pages, 2 figures, presented at SPIE Symposium "Astronomical Telescopes and Instrumentation'' conference "Adaptive Optics Systems II'',Sunday 27 June 2010, San Diego, California, US

Automatically Predicting User Ratings for Conversational Systems

Automatic evaluation models for open-domain conversational agents either correlate poorly with human judgment or require expensive annotations on top of conversation scores. In this work we investigate the feasibility of learning evaluation models without relying on any further annotations besides conversation-level human ratings. We use a dataset of rated (1-5) open domain spoken conversations between the conversational agent Roving Mind (competing in the Amazon Alexa Prize Challenge 2017) and Amazon Alexa users. First, we assess the complexity of the task by asking two experts to re-annotate a sample of the dataset and observe that the subjectivity of user ratings yields a low upper-bound. Second, through an analysis of the entire dataset we show that automatically extracted features such as user sentiment, Dialogue Acts and conversation length have significant, but low correlation with user ratings. Finally, we report the results of our experiments exploring different combinations of these features to train automatic dialogue evaluation models. Our work suggests that predicting subjective user ratings in open domain conversations is a challenging task.I modelli stato dell’arte per la valutazione automatica di agenti conversazionali open-domain hanno una scarsa correlazione con il giudizio umano oppure richiedono costose annotazioni oltre al punteggio dato alla conversazione. In questo lavoro investighiamo la possibilità di apprendere modelli di valutazione attraverso il solo utilizzo di punteggi umani dati all’intera conversazione. Il corpus utilizzato è composto da conversazioni parlate open-domain tra l’agente conversazionale Roving Mind (parte della competizione Amazon Alexa Prize 2017) e utenti di Amazon Alexa valutate con punteggi da 1 a 5. In primo luogo, valutiamo la complessità del task assegnando a due esperti il compito di riannotare una parte del corpus e osserviamo come esso risulti complesso perfino per annotatori umani data la sua soggettività. In secondo luogo, tramite un’analisi condotta sull’intero corpus mostriamo come features estratte automaticamente (sentimento dell’utente, Dialogue Acts e lunghezza della conversazione) hanno bassa, ma significativa correlazione con il giudizio degli utenti. Infine, riportiamo i risultati di esperimenti volti a esplorare diverse combinazioni di queste features per addestrare modelli di valutazione automatica del dialogo. Questo lavoro mostra la difficoltà del predire i giudizi soggettivi degli utenti in conversazioni senza un task specifico

Magellan Adaptive Optics first-light observations of the exoplanet beta Pic b. II. 3-5 micron direct imaging with MagAO+Clio, and the empirical bolometric luminosity of a self-luminous giant planet

Young giant exoplanets are a unique laboratory for understanding cool, low-gravity atmospheres. A quintessential example is the massive extrasolar planet $\beta$ Pic b, which is 9 AU from and embedded in the debris disk of the young nearby A6V star $\beta$ Pictoris. We observed the system with first light of the Magellan Adaptive Optics (MagAO) system. In Paper I we presented the first CCD detection of this planet with MagAO+VisAO. Here we present four MagAO+Clio images of $\beta$ Pic b at 3.1 $\mu$m, 3.3 $\mu$m, $L^\prime$, and $M^\prime$, including the first observation in the fundamental CH$_4$ band. To remove systematic errors from the spectral energy distribution (SED), we re-calibrate the literature photometry and combine it with our own data, for a total of 22 independent measurements at 16 passbands from 0.99--4.8 $\mu$m. Atmosphere models demonstrate the planet is cloudy but are degenerate in effective temperature and radius. The measured SED now covers $>$80\% of the planet's energy, so we approach the bolometric luminosity empirically. We calculate the luminosity by extending the measured SED with a blackbody and integrating to find log($L_{bol}$/$L_{Sun}$) $= -3.78\pm0.03$. From our bolometric luminosity and an age of 23$\pm$3 Myr, hot-start evolutionary tracks give a mass of 12.7$\pm$0.3 $M_{Jup}$, radius of 1.45$\pm$0.02 $R_{Jup}$, and $T_{eff}$ of 1708$\pm$23 K (model-dependent errors not included). Our empirically-determined luminosity is in agreement with values from atmospheric models (typically $-3.8$ dex), but brighter than values from the field-dwarf bolometric correction (typically $-3.9$ dex), illustrating the limitations in comparing young exoplanets to old brown dwarfs.Comment: Accepted to ApJ. 27 pages, 22 figures, 19 table

On the Morphology and Chemical Composition of the HR 4796A Debris Disk

[abridged] We present resolved images of the HR 4796A debris disk using the Magellan adaptive optics system paired with Clio-2 and VisAO. We detect the disk at 0.77 \microns, 0.91 \microns, 0.99 \microns, 2.15 \microns, 3.1 \microns, 3.3 \microns, and 3.8 \microns. We find that the deprojected center of the ring is offset from the star by 4.76$\pm$1.6 AU and that the deprojected eccentricity is 0.06$\pm$0.02, in general agreement with previous studies. We find that the average width of the ring is 14$^{+3}_{-2}$, also comparable to previous measurements. Such a narrow ring precludes the existence of shepherding planets more massive than \about 4 \mj, comparable to hot-start planets we could have detected beyond \about 60 AU in projected separation. Combining our new scattered light data with archival HST/STIS and HST/NICMOS data at \about 0.5-2 \microns, along with previously unpublished Spitzer/MIPS thermal emission data and all other literature thermal data, we set out to constrain the chemical composition of the dust grains. After testing 19 individual root compositions and more than 8,400 unique mixtures of these compositions, we find that good fits to the scattered light alone and thermal emission alone are discrepant, suggesting that caution should be exercised if fitting to only one or the other. When we fit to both the scattered light and thermal emission simultaneously, we find mediocre fits (reduced chi-square \about 2). In general, however, we find that silicates and organics are the most favored, and that water ice is usually not favored. These results suggest that the common constituents of both interstellar dust and solar system comets also may reside around HR 4796A, though improved modeling is necessary to place better constraints on the exact chemical composition of the dust.Comment: Accepted to ApJ on October 27, 2014. 21 pages, 12 figures, 4 table