Three-phase equilibria of hydrates from computer simulation. I. Finite-size effects in the methane hydrate

Clathrate hydrates are vital in energy research and environmental applications. Understanding their stability is crucial for harnessing their potential. In this work, we employ direct coexistence simulations to study finite-size effects in the determination of the three-phase equilibrium temperature (T3) for methane hydrates. Two popular water models, TIP4P/Ice and TIP4P/2005, are employed, exploring various system sizes by varying the number of molecules in the hydrate, liquid, and gas phases. The results reveal that finite-size effects play a crucial role in determining T3. The study includes nine configurations with varying system sizes, demonstrating that smaller systems, particularly those leading to stoichiometric conditions and bubble formation, may yield inaccurate T3 values. The emergence of methane bubbles within the liquid phase, observed in smaller configurations, significantly influences the behavior of the system and can lead to erroneous temperature estimations. Our findings reveal finite-size effects on the calculation of T3 by direct coexistence simulations and clarify the system size convergence for both models, shedding light on discrepancies found in the literature. The results contribute to a deeper understanding of the phase equilibrium of gas hydrates and offer valuable information for future research in this field.

Madrid-2019 force field: An extension to divalent cations Sr2+ and Ba2

In this work, we present a parameterization of Sr2+ and Ba2+ cations, which expands the alkali earth set of cations of the Madrid-2019 force field. We have tested the model against the experimental densities of eight different salts, namely, SrCl2, SrBr2, SrI2, Sr(NO3)2, BaCl2, BaBr2, BaI2, and Ba(NO3)2. The force field is able to reproduce the experimental densities of all these salts up to their solubility limit. Furthermore, we have computed the viscosities for two selected salts, finding that the experimental values are overestimated, but the predictions are still reasonable. Finally, the structural properties for all the salts have been calculated with this model and align remarkably well with experimental observations.

Growth rate of CO2 and CH4 hydrates by means of molecular dynamics simulations

CO2 and CH4 hydrates are of great importance both from an energetic and from an environmental point of view. It is therefore highly relevant to quantify and understand the rate with which they grow. We use molecular dynamics simulations to shed light on the growth rate of these hydrates. We put the solid hydrate phase in contact with a guest aqueous solution in equilibrium with the pure guest phase and study the growth of both hydrates at 400 bars with temperature. We compare our results with previous calculations of the ice growth rate. We find a growth rate maximum as a function of the supercooling in all cases. The incorporation of guest molecules into the solid structure strongly decelerates hydrate growth. Consistently, ice grows faster than either hydrate and the CO2 hydrate grows faster than the CH4 one because of the higher solubility of CO2. We also quantify the molecular motion required to build the solids under study and find that the distance traveled by liquid molecules exceeds by orders of magnitude that advanced by any solid. Less molecular motion is needed in order for ice to grow as compared to the hydrates. Moreover, when temperature increases, more motion is needed for solid growth. Finally, we find a good agreement between our growth rate calculations and experiments of hydrate growth along the guest-solution interface. However, more work is needed to reconcile experiments of hydrate growth toward the solution among each other and with simulations.

Minimum in the pressure dependence of the interfacial free energy between ice Ih and water

Despite the importance of ice nucleation, this process has been barely explored at negative pressures. Here, we study homogeneous ice nucleation in stretched water by means of molecular dynamics seeding simulations using the TIP4P/Ice model. We observe that the critical nucleus size, interfacial free energy, free energy barrier, and nucleation rate barely change between isobars from -2600 to 500 bars when they are represented as a function of supercooling. This allows us to identify universal empirical expressions for homogeneous ice nucleation in the pressure range from -2600 to 500 bars. We show that this universal behavior arises from the pressure dependence of the interfacial free energy, which we compute by means of the mold integration technique, finding a shallow minimum around -2000 bars. Likewise, we show that the change in the interfacial free energy with pressure is proportional to the excess entropy and the slope of the melting line, exhibiting in the latter a reentrant behavior also at the same negative pressure. Finally, we estimate the excess internal energy and the excess entropy of the ice Ih-water interface.

Homogeneous nucleation rate of methane hydrate formation under experimental conditions from seeding simulations

In this work, we shall estimate via computer simulations the homogeneous nucleation rate for the methane hydrate at 400 bars for a supercooling of about 35 K. The TIP4P/ICE model and a Lennard-Jones center were used for water and methane, respectively. To estimate the nucleation rate, the seeding technique was employed. Clusters of the methane hydrate of different sizes were inserted into the aqueous phase of a two-phase gas-liquid equilibrium system at 260 K and 400 bars. Using these systems, we determined the size at which the cluster of the hydrate is critical (i.e., it has 50% probability of either growing or melting). Since nucleation rates estimated from the seeding technique are sensitive to the choice of the order parameter used to determine the size of the cluster of the solid, we considered several possibilities. We performed brute force simulations of an aqueous solution of methane in water in which the concentration of methane was several times higher than the equilibrium concentration (i.e., the solution was supersaturated). From brute force runs, we infer the value of the nucleation rate for this system rigorously. Subsequently, seeding runs were carried out for this system, and it was found that only two of the considered order parameters were able to reproduce the value of the nucleation rate obtained from brute force simulations. By using these two order parameters, we estimated the nucleation rate under experimental conditions (400 bars and 260 K) to be of the order of log₁₀ (J/(m³ s)) = -7(5).

Scaled charges for ions: An improvement but not the final word for modeling electrolytes in water

In this work, we discuss the use of scaled charges when developing force fields for NaCl in water. We shall develop force fields for Na⁺ and Cl^- using the following values for the scaled charge (in electron units): ±0.75, ±0.80, ±0.85, and ±0.92 along with the TIP4P/2005 model of water (for which previous force fields were proposed for q = ±0.85 and q = ±1). The properties considered in this work are densities, structural properties, transport properties, surface tension, freezing point depression, and maximum in density. All the developed models were able to describe quite well the experimental values of the densities. Structural properties were well described by models with charges equal to or larger than ±0.85, surface tension by the charge ±0.92, maximum in density by the charge ±0.85, and transport properties by the charge ±0.75. The use of a scaled charge of ±0.75 is able to reproduce with high accuracy the viscosities and diffusion coefficients of NaCl solutions for the first time. We have also considered the case of KCl in water, and the results obtained were fully consistent with those of NaCl. There is no value of the scaled charge able to reproduce all the properties considered in this work. Although certainly scaled charges are not the final word in the development of force fields for electrolytes in water, its use may have some practical advantages. Certain values of the scaled charge could be the best option when the interest is to describe certain experimental properties.

P-177 Non-invasive aneuploidy testing versus conventional morphological embryo selection in good prognosis patients

Study question

Can non-invasive preimplantation genetic testing of aneuploidies (niPGT-A) improve the clinical outcome in good prognosis patients compared to morphological embryo selection without aneuploidy testing?

Summary answer

Embryonic cell-free DNA (cfDNA) in the blastocyst culture medium offers more objective information for blastocyst selection, resulting in higher ongoing pregnancy rate in good-prognosis patients.

What is known already

One of the biggest challenges in IVF is accurately selecting viable embryos that are most likely to produce a healthy child at home after embryo transfer. Trophectoderm biopsy and PGT-A have improved implantation and clinical pregnancy rates per transfer; however, two recent studies have shown that PGTA does not improve clinical pregnancy rates below 35 years. A non-invasive alternative is to analyze (the cfDNA) in blastocyst culture medium. Several studies have shown that cfDNA testing on blastocyst culture medium at day 6 of development allows detection of aneuploidies with high concordance rates compared to TE biopsy and inner cell mass

Study design, size, duration

This observational study reports data from September 2020 to December 2021. During this period, niPGT-A was performed on 25 patients under 35 years of age whit average age of 32, where cfDNA analysis was applied to the culture medium of 92 blastocysts. A total of 20 single embryo transfers (SETs) have been performed so far, comparing the results with 31 transfers performed in the same period based only on morphological criteria.

Participants/materials, setting, methods

In the niPGT-A group, embryos were cultured in a Geri incubator up to day-4, and then individually cultured in 10 µl drops of CCSS (Fujifilm) until day 6 in an ESCO –system whit low oxygen concentration. At day-6, blastocysts were vitrified, and media collected in sterile PCR tubes after at least 40 hours in culture. After collection, media were immediately frozen and analyzed by Next Generation Sequencing analysis. Deferred transfer was performed according to media results.

Main results and the role of chance

In the niPGT-A group euploidy rate was 57% whit 8% non- informative results. Pregnancy rate was 80% with 75% ongoing pregnancy and 5% miscarriage rates, having 8 live births up to now. For the morphology group, pregnancy rate was 58% with 55% ongoing pregnancy and 3% miscarriage rates.

We did a secondary analysis identifiying which blastocyst we would be transfered, if only morphology would be considered. We observed that in 65% of the cases we would choose the same embryo as with niPGT-A, however in 35% of the cases we would have transferred a blastocyst with an aneuploid medium. Regarding blastocyst quality for throphoectoderm classified as A,B or C the euploidy rate were 62%,58% and 33% respectively, and pregnancy rates were 100%, 78% and 33%. For inne cell mass, similar euploidy rates werw observed for blastocyst classified as A,B or C (59%,52% and 57% respectively) and pregnancy rates were 100%, 73% and 100%. Evaluating the expansion grade in blastocoel no differences were observed in euploidy rates for cathegories 4, 5 and 6 (52%, 54% and 50% respectively) and pregnancy rates were 82%, 100% and 100%. We observed the lower pregnancy rate for blastocysts whit throphoectoderm C previously suggested by other authors.

Limitations, reasons for caution

Our results are encouraging since this group of good prognosis could improve their ongoing pregnancy rate even having a good reproductive prognosis whit morphology selection. Larger randomized controlled trials are needed to verify and extend our findings in this age range

Wider implications of the findings

These results support the clinical application of niPGT-A in the laboratory routine as a proritization tool, without the need of embryo manipulation, reducing subjectivity for blastocyst selection compared to morphology and increasing the ongoing pregnancy rate in good prognosis patients

Trial registration number

Sa-16552/19-EC:428

Melting points of water models: Current situation

By using the direct coexistence method, we have calculated the melting points of ice I h at normal pressure for three recently proposed water models, namely, TIP3P-FB, TIP4P-FB, and TIP4P-D. We obtained T m = 216 K for TIP3P-FB, T m = 242 K for TIP4P-FB, and T m = 247 K for TIP4P-D. We revisited the melting point of TIP4P/2005 and TIP5P obtaining T m = 250 and 274 K, respectively. We summarize the current situation of the melting point of ice I h for a number of water models and conclude that no model is yet able to simultaneously reproduce the melting temperature of ice I h and the temperature of the maximum in density at room pressure. This probably points toward our both still incomplete knowledge of the potential energy surface of water and the necessity of incorporating nuclear quantum effects to describe both properties simultaneously.

Maximum in density of electrolyte solutions: Learning about ion-water interactions and testing the Madrid-2019 force field

In this work, we studied the effect of Li⁺, Na⁺, K⁺, Mg²⁺, and Ca²⁺ chlorides and sulfates on the temperature of maximum density (TMD) of aqueous solutions at room pressure. Experiments at 1 molal salt concentration were carried out to determine the TMD of these solutions. We also performed molecular dynamics simulations to estimate the TMD at 1 and 2 m with the Madrid-2019 force field, which uses the TIP4P/2005 water model and scaled charges for the ions, finding an excellent agreement between experiment and simulation. All the salts studied in this work shift the TMD of the solution to lower temperatures and flatten the density vs temperature curves (when compared to pure water) with increasing salt concentration. The shift in the TMD depends strongly on the nature of the electrolyte. In order to explore this dependence, we have evaluated the contribution of each ion to the shift in the TMD concluding that Na⁺, Ca²⁺, and SO₄ ^2- seem to induce the largest changes among the studied ions. The volume of the system has been analyzed for salts with the same anion and different cations. These curves provide insight into the effect of different ions upon the structure of water. We claim that the TMD of electrolyte solutions entails interesting physics regarding ion-water and water-water interactions and should, therefore, be considered as a test property when developing force fields for electrolytes. This matter has been rather unnoticed for almost a century now and we believe it is time to revisit it.

On the thermodynamics of curved interfaces and the nucleation of hard spheres in a finite system

We determine, for hard spheres, the Helmholtz free energy of a liquid that contains a solid cluster as a function of the size of the solid cluster by means of the formalism of the thermodynamics of curved interfaces. This is done at the constant total number of particles, volume, and temperature. We show that under certain conditions, one may have several local minima in the free energy profile, one for the homogeneous liquid and others for the spherical, cylindrical, and planar solid clusters surrounded by liquid. The variation of the interfacial free energy with the radius of the solid cluster and the distance between equimolar and tension surfaces are inputs from simulation results of nucleation studies. This is possible because stable solid clusters in the canonical ensemble become critical in the isothermal-isobaric ensemble. At each local minimum, we find no difference in chemical potential between the phases. At local maxima, we also find equal chemical potential, albeit in this case the nucleus is unstable. Moreover, the theory allows us to describe the stable solid clusters found in simulations. Therefore, we can use it for any combination of the total number of particles, volume, and global density as long as a minimum in the Helmholtz free energy occurs. We also study under which conditions the absolute minimum in the free energy corresponds to a homogeneous liquid or to a heterogeneous system having either spherical, cylindrical, or planar geometry. This work shows that the thermodynamics of curved interfaces at equilibrium can be used to describe nucleation.

Homogeneous nucleation of NaCl in supersaturated solutions

The seeding method is an approximate approach to investigate nucleation that combines molecular dynamics simulations with classical nucleation theory. Recently, this technique has been successfully implemented in a broad range of nucleation studies. However, its accuracy is subject to the arbitrary choice of the order parameter threshold used to distinguish liquid-like from solid-like molecules. We revisit here the crystallization of NaCl from a supersaturated brine solution and show that consistency between seeding and rigorous methods, like Forward Flux Sampling (from previous work) or spontaneous crystallization (from this work), is achieved by following a mislabelling criterion to select such threshold (i.e. equaling the fraction of the mislabelled particles in the bulk parent and nucleating phases). This work supports the use of seeding to obtain fast and reasonably accurate nucleation rate estimates and the mislabelling criterion as one giving the relevant cluster size for classical nucleation theory in crystallization studies.

Critical COVID-19 rarely associated with left ventricular systolic impairment

Introduction

For some individuals infection with SARS-CoV-2 leading to COVID-19 can result in a life-threatening multi-system disease. Multiple potential pathophysiological mechanisms for the development of cardiovascular complications have been postulated [1]. Early reports suggested that more than a third of hospitalised patients undergoing TTE had evidence of LV impairment [2].

Purpose

To ascertain the incidence of ventricular impairment among critically ill adults with COVID-19 admitted to the intensive care unit (ICU).

Methods

Retrospective analysis of transthoracic echocardiograms (TTE) performed on patients admitted to ICU with COVID-19 between 10th March and 10th May 2020. Archived studies were reviewed by accredited professionals. Studies were performed according to a modified British Society of Echocardiography (BSE) Level 1 protocol [3], with the addition of right ventricle (RV) focused apical 4 chamber, as well as apical 2 and 3 chamber views, and without ECG synchronisation as per infection control protocols. In the majority of patients the left ventricular ejection fraction (LVEF) was estimated from biplane Simpson's method. The RV function was assessed using the TAPSE in most patients. In the remaining patients the LV or RV function was visually assessed.

Results

Of 179 patients admitted to ICU, 85 (47.5%) had at least one TTE of diagnostic quality. Studies were performed a median of 7 days after ICU admission (IQR 3–17 days). Baseline and clinical characteristics and key echocardiographic measurements are summarised in table 1. The majority of patients were undergoing mechanical ventilation at the time of the scan (94.1%). One hundred and fifty-nine patients (89%) had elevated Troponin T (≥14ng/L) on the day of the study. LV systolic impairment (LVSD) was present in 5 patients (6.0%). This was known to be chronic in 3 patients (1 with coronary artery disease, 1 with chemotherapy induced cardiomyopathy and 1 with dilated cardiomyopathy of unknown aetiology), whilst pre-morbid cardiac function was unknown in the other 2 patients. No patient had severe LVSD (LVEF ≤35%). RV systolic dysfunction (RVSD) was found in 25 patients (31.3%). Amongst patients receiving mechanical ventilation there was no significant difference in Positive End Expiratory Pressure (PEEP) between patients with and without RVSD (9.4cmH2O vs. 9.8cmH2O, p=0.64), however there was a non-significant trend towards lower PaO2/FiO2 (P/F ratio) amongst patients with RVSD (18.9kPa vs 25.7kPa, p=0.07).

Conclusions

In contrast to other studies which have reported high frequency of LV impairment amongst hospitalised patients with COVID-19 [3], de novo LVSD was rarely found in this study, occurring in just 2 patients (2.4%), and being severe in neither. RV dilatation and systolic impairment were commonly found. A trend towards lower P/F ratios in patients with RVSD suggests severity of lung injury may be a factor in developing RV impairment.

Funding Acknowledgement

Type of funding sources: None.

Molecular characterization of group A rotavirus strains detected in alpacas (Vicugna pacos) from Peru

The alpaca is a very important social and economic resource for the production of fibre and meat for Andean communities. Peru is the main producer of alpacas. Group A rotavirus (RVA) has been sporadically detected in alpacas. In this study, a total of 1423 faecal samples from alpacas from different locations of the Puno department in Peru were collected and analysed by an antigen-capture ELISA in order to detect RVA. Four per cent of the samples were RVA-positive (57/1423). The genotype constellation of three selected alpaca RVA strains were G3/8 P[1/14]-I2-R2/5-C2/3-M2/3-A17-N2/3-T6-E3-H3. Two of the analysed strains presented a bovine-like genotype constellation, whereas the third strain presented six segments belonging to the AU-1-like genogroup (G3, M3, C3, N3, T3 and E3), suggesting reassorting events. Monitoring of the sanitary health of juvenile alpacas is essential to reduce the rates of neonatal mortality and for the development of preventive health strategies.

Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus

BACKGROUND

Vaccines comprising recombinant subunit proteins are well-suited to low-cost and high-volume production for global use. The design of manufacturing processes to produce subunit vaccines depends, however, on the inherent biophysical traits presented by an individual antigen of interest. New candidate antigens typically require developing custom processes for each one and may require unique steps to ensure sufficient yields without product-related variants.

RESULTS

We describe a holistic approach for the molecular design of recombinant protein antigens-considering both their manufacturability and antigenicity-informed by bioinformatic analyses such as RNA-seq, ribosome profiling, and sequence-based prediction tools. We demonstrate this approach by engineering the product sequences of a trivalent non-replicating rotavirus vaccine (NRRV) candidate to improve titers and mitigate product variants caused by N-terminal truncation, hypermannosylation, and aggregation. The three engineered NRRV antigens retained their original antigenicity and immunogenicity, while their improved manufacturability enabled concomitant production and purification of all three serotypes in a single, end-to-end perfusion-based process using the biotechnical yeast Komagataella phaffii.

CONCLUSIONS

This study demonstrates that molecular engineering of subunit antigens using advanced genomic methods can facilitate their manufacturing in continuous production. Such capabilities have potential to lower the cost and volumetric requirements in manufacturing vaccines based on recombinant protein subunits.

Development of a platform process for the production and purification of single-domain antibodies

Single‐domain antibodies (sdAbs) offer the affinity and therapeutic value of conventional antibodies, with increased stability and solubility. Unlike conventional antibodies, however, sdAbs do not benefit from a platform manufacturing process. While successful production of a variety of sdAbs has been shown in numerous hosts, purification methods are often molecule specific or require affinity tags, which generally cannot be used in clinical manufacturing due to regulatory concerns. Here, we have developed a broadly applicable production and purification process for sdAbs in Komagataella phaffii (Pichia pastoris) and demonstrated the production of eight different sdAbs at a quality appropriate for nonclinical studies. We developed a two‐step, integrated purification process without the use of affinity resins and showed that modification of a single process parameter, pH of the bridging buffer, was required for the successful purification of a variety of sdAbs. Further, we determined that this parameter can be predicted based only on the biophysical characteristics of the target molecule. Using these methods, we produced nonclinical quality sdAbs as few as 5 weeks after identifying the product sequence. Nonclinical studies of three different sdAbs showed that molecules produced using our platform process conferred protection against viral shedding of rotavirus or H1N1 influenza and were equivalent to similar molecules produced in Escherichia coli and purified using affinity tags.

Influence of individual or group housing of newborn calves on rotavirus and coronavirus infection during the first 2 months of life

Bovine rotavirus A (RVA) and bovine coronavirus (CoV) are the two main viral enteropathogens associated with neonatal calf diarrhea. The aim of the present work was to study the impact of group and individual housing systems in the epidemiology of RVA and CoV infection. Eleven calves reared in individual housing (FA) and nine calves in group housing (FB) were monitored during the first 7 weeks of life. Stool and serum samples were screened for RVA and CoV antigens by ELISA. IgG1 antibodies (Ab) to both antigens were also measured. From the 160 fecal samples collected, the proportion of positive samples to RVA and CoV was significantly higher in FB (23.6%) than in FA (9%) (p = 0.03). The geometric mean of colostral IgG1 Ab titers to CoV and RVA in FA (IgG1 anti-CoV 1024 and anti-RVA 1782.9) was lower than in FB (IgG1 anti-CoV 10,321.2 and anti-RVA 4096) at birth. Calves less than 2 weeks of life from FB had a higher risk of being infected by RVA (OR = 4.9; p = 0.01) and CoV (OR = 17.15; p = 0.01) than calves from FA. The obtained results showed that there was higher RVA and CoV shedding in group-housed calves than in individual-housed animals.

Equivalence between condensation and boiling in a Lennard-Jones fluid

Condensation and boiling are phase transitions highly relevant to industry, geology, and atmospheric science. These phase transitions are initiated by the nucleation of a drop in a supersaturated vapor and of a bubble in an overstretched liquid, respectively. The surface tension between both phases, liquid and vapor, is a key parameter in the development of such nucleation stage. Whereas the surface tension can be readily measured for a flat interface, there are technical and conceptual limitations to obtain it for the curved interface of the nucleus. On the technical side, it is quite difficult to observe a critical nucleus in experiments. From a conceptual point of view, the interfacial free energy depends on the choice of the dividing surface, being the surface of tension the one relevant for nucleation. We bypass the technical limitation by performing simulations of a Lennard-Jones fluid where we equilibrate critical nuclei (both drops and bubbles). Regarding the conceptual hurdle, we find the relevant cluster size by searching the radius that correctly predicts nucleation rates and nucleation free energy barriers when combined with Classical Nucleation Theory. With such definition of the cluster size we find the same value of the surface tension for drops and bubbles of a given radius. Thus, condensation and boiling can be viewed as two sides of the same coin. Finally, we combine the data coming from drops and bubbles to obtain, via two different routes, estimates of the Tolman length, a parameter that allows describing the curvature dependence of the surface tension in a theoretical framework.

First report of group A rotavirus and bovine coronavirus associated with neonatal calf diarrhea in the northwest of Argentina

Group A rotavirus (RVA) and bovine coronavirus (BCoV) are the two main viral enteropathogens associated with neonatal calf diarrhea. The aim of the present survey was to investigate the epidemiology and the role of RVA and BCoV in the presentation of dairy and beef calf diarrhea in Lerma Valley of Salta province, within the Northwest region of Argentina. Stool samples of calves with or without diarrhea younger than 2 months of age were collected from 19 dairy farms and 20 beef farms between the years 2014 and 2016. Stool samples were screened for RVA and BCoV detection by ELISA. Heminested multiplex RT-PCR was used for RVA typing and RT-PCR to confirm BCoV. Positive samples were submitted to sequencing analysis. Bovine RVA and BCoV were circulating in 63% (12/19) and 10.52% (2/19) of the dairy farms, respectively, where 9.5% (46/484) of the calves were positives to RVA and 0.4% (2/484) to BCoV. In beef herds, RVA was detected in 40% (8/20) of the farms and in 6.75% (21/311) of the calves, without positives cases of BCoV. Molecular analysis showed that in dairy farms, G6P[11] and G10P[11] were the prevalent RVA strains, while in beef farms, G10P[11] was the prevalent. The main finding was the detection for the first time of a G15P[11] causing diarrhea in beef calves of Argentina that represents a new alert to be consider for future vaccine updates. Analysis of detected BCoV showed that it is related to the other circulating strains of Argentina.

Seeding approach to nucleation in the NVT ensemble: The case of bubble cavitation in overstretched Lennard Jones fluids

Simulations are widely used to study nucleation in first order phase transitions due to the fact that they have access to the relevant length and time scales. However, simulations face the problem that nucleation is an activated process. Therefore, rare event simulation techniques are needed to promote the formation of the critical nucleus. The Seeding method, where the simulations are started with the nucleus already formed, has proven quite useful in efficiently providing estimates of the nucleation rate for a wide range of orders of magnitude. So far, Seeding has been employed in the NPT ensemble, where the nucleus either grows or redissolves. Thus, several trajectories have to be run in order to find the thermodynamic conditions that make the seeded nucleus critical. Moreover, the nucleus lifetime is short and the statistics for obtaining its properties is consequently poor. To deal with these shortcomings we extend the Seeding method to the NVT ensemble. We focus on the problem of bubble nucleation in a metastable Lennard Jones fluid. We show that, in the NVT ensemble, it is possible to equilibrate and stabilise critical bubbles for a long time. The nucleation rate inferred from NVT-Seeding is fully consistent with that coming from NPT-Seeding. The former is quite suitable to obtain the nucleation rate along isotherms, whereas the latter is preferable if the dependence of the rate with temperature at constant pressure is required. Care should be taken with finite size effects when using NVT-Seeding. Further work is required to extend NVT seeding to other sorts of phase transitions.

Seeding approach to bubble nucleation in superheated Lennard-Jones fluids

We investigate vapor homogeneous nucleation in a superheated Lennard-Jones liquid with computer simulations. Special simulation techniques are required to address this study since the nucleation of a critical vapor bubble-one that has an equal chance to grow or shrink-in a moderately superheated liquid is a rare event. We use the Seeding method, which combines Classical Nucleation Theory with computer simulations of a liquid containing a vapor bubble to provide bubble nucleation rates in a wide temperature range. Seeding has been successfully applied to investigate the nucleation of crystals in supercooled fluids, and here we apply it to the liquid-to-vapor transition. We find that the Seeding method provides nucleation rates that are consistent with independent calculations not based on the assumptions of Classical Nucleation Theory. Different criteria to determine the radius of the critical bubble give different rate values. The accuracy of each criterion depends of the degree of superheating. Moreover, seeding simulations show that the surface tension depends on pressure for a given temperature. Therefore, using Classical Nucleation Theory with the coexistence surface tension does not provide good estimates of the nucleation rate.

A force field of Li+, Na+, K+, Mg2+, Ca2+, Cl-, and SO4 2- in aqueous solution based on the TIP4P/2005 water model and scaled charges for the ions

In this work, a force field for several ions in water is proposed. In particular, we consider the cations Li⁺, Na⁺, K⁺, Mg²⁺, and Ca²⁺ and the anions Cl^- and SO₄ ^2-. These ions were selected as they appear in the composition of seawater, and they are also found in biological systems. The force field proposed (denoted as Madrid-2019) is nonpolarizable, and both water molecules and sulfate anions are rigid. For water, we use the TIP4P/2005 model. The main idea behind this work is to further explore the possibility of using scaled charges for describing ionic solutions. Monovalent and divalent ions are modeled using charges of 0.85 and 1.7, respectively (in electron units). The model allows a very accurate description of the densities of the solutions up to high concentrations. It also gives good predictions of viscosities up to 3 m concentrations. Calculated structural properties are also in reasonable agreement with the experiment. We have checked that no crystallization occurred in the simulations at concentrations similar to the solubility limit. A test for ternary mixtures shows that the force field provides excellent performance at an affordable computer cost. In summary, the use of scaled charges, which could be regarded as an effective and simple way of accounting for polarization (at least to a certain extend), improves the overall description of ionic systems in water. However, for purely ionic systems, scaled charges will not adequately describe neither the solid nor the melt.

On the time required to freeze water

By using the seeding technique the nucleation rate for the formation of ice at room pressure will be estimated for the TIP4P/ICE model using longer runs and a smaller grid of temperatures than in the previous work. The growth rate of ice will be determined for TIP4P/ICE and for the mW model of water. Although TIP4P/ICE and mW have a similar melting point and melting enthalpy, they differ significantly in the dynamics of freezing. The nucleation rate of mW is lower than that of TIP4P/ICE due to its higher interfacial free energy. Experimental results for the nucleation rate of ice are between the predictions of these two models when obtained from the seeding technique, although closer to the predictions of TIP4P/ICE. The growth rate of ice for the mW model is four orders of magnitude larger than for TIP4P/ICE. Avrami's expression is used to estimate the crystallization time from the values of the nucleation and growth rates. For mW the minimum in the crystallization time is found at approximately 85 K below the melting point and its value is of about a few ns, in agreement with the results obtained from brute force simulations by Moore and Molinero. For the TIP4P/ICE the minimum is found at about 55 K below the melting point, but its value is about ten microseconds. This value is compatible with the minimum cooling rate required to avoid the formation of ice and obtaining a glass phase. The crossover from the nucleation controlled crystallization to the growth controlled crystallization will be discussed for systems of finite size. This crossover could explain the apparent discrepancy between the values of J obtained by different experimental groups for temperatures below 230 K and should be considered as an alternative hypothesis to the two previously suggested: internal pressure and/or surface freezing effects. A maximum in the compressibility was found for the TIP4P/ICE model in supercooled water. The relaxation time is much smaller than the crystallization time at the temperature at which this maximum occurs, so this maximum is a real thermodynamic feature of the model. At the temperature of minimum crystallization time, the crystallization time is larger than the relaxation time by just two orders of magnitude.

A new intermolecular potential for simulations of methanol: The OPLS/2016 model

In this work, a new rigid-nonpolarizable model of methanol is proposed. The model has three sites, located at the same positions as those used in the OPLS model previously proposed by Jorgensen [J. Phys. Chem. 90, 1276 (1986)]. However, partial charges and the values of the Lennard-Jones parameters were modified by fitting to an adequately selected set of target properties including solid-fluid experimental data. The new model was denoted as OPLS/2016. The overall performance of this model was evaluated and compared to that obtained with other popular models of methanol using a similar test to that recently proposed for water models. In the test, a certain numerical score is given to each model. It was found that the OPLS/2016 obtained the highest score (7.4 of a maximum of 10) followed by L1 (6.6), L2 (6.4), OPLS (5.8), and H1 (3.5) models. The improvement of OPLS/2016 with respect to L1 and L2 is mainly due to an improvement in the description of fluid-solid equilibria (the melting point is only 14 K higher than the experimental value). In addition, it was found that no methanol model was able to reproduce the static dielectric constant and the isobaric heat capacity, whereas the better global performance was found for models that reproduce the vaporization enthalpy once the so-called polarization term is included. Similar conclusions were suggested previously in the analysis of water models and are confirmed here for methanol.

Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route

The solubility of NaCl in water is evaluated by using three force field models: Joung-Cheatham for NaCl dissolved in two different water models (SPC/E and TIP4P/2005) and Smith Dang NaCl model in SPC/E water. The methodology based on free-energy calculations [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] and [J. L. Aragones et al., J. Chem. Phys. 136, 244508 (2012)] has been used, except, that all calculations for the NaCl in solution were obtained by using molecular dynamics simulations with the GROMACS package instead of homemade MC programs. We have explored new lower molalities and made longer runs to improve the accuracy of the calculations. Exploring the low molality region allowed us to obtain an analytical expression for the chemical potential of the ions in solution as a function of molality valid for a wider range of molalities, including the infinite dilute case. These new results are in better agreement with recent estimations of the solubility obtained with other methodologies. Besides, two empirical simple rules have been obtained to have a rough estimate of the solubility of a certain model, by analyzing the ionic pairs formation as a function of molality and/or by calculating the difference between the NaCl solid chemical potential and the standard chemical potential of the salt in solution.

Molecular and antigenic characterization of bovine Coronavirus circulating in Argentinean cattle during 1994-2010

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Detection rate of BCoV was statistically higher in dairy than in beef calves.

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Argentinean strains are distant from the Mebus strain included in local vaccines.

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In vitro cross-protection between Arg95 field strain and Mebus reference strain.

Bovine coronavirus (BCoV) is an important viral pathogen associated with neonatal calf diarrhea. Our aim was to investigate the incidence of BCoV in diarrhea outbreaks in beef and dairy herds from Argentina during 1994–2010. A total of 5.365 fecal samples from diarrheic calves were screened for BCoV diagnosis by ELISA. The virus was detected in 1.71% (92/5365) of the samples corresponding to 5.95% (63/1058) of the diarrhea cases in 239 beef and 324 dairy farms. The detection rate of BCoV was significantly higher in dairy than in beef herds: 12.13% (29/239) vs. 4.32% (14/324) respectively. Phylogenetic analysis of the hypervariable S1 region of seven representative samples (from different husbandry systems, farm locations and years of sampling) indicated that BCoV strains circulating in Argentinean beef and dairy herds formed a cluster distinct from other geographical regions. Interestingly, Argentinean strains are distantly related (at both the nucleotide and amino acid levels) with the Mebus historic reference BCoV strain included in the vaccines currently available in Argentina. However, Mebus-induced antibodies were capable of neutralizing the BCoV Arg95, a field strain adapted to grow in vitro, and vice versa, indicating that both strains belong to the same CoV serotype reported in cattle. This work represents the first large survey describing BCoV circulation in Argentinean cattle.

Egg yolk IgY antibodies: A therapeutic intervention against group A rotavirus in calves

Bovine group A rotavirus (RVA) is considered the major cause of diarrhea in intensively reared neonatal calves. Chicken egg yolk antibodies (IgY) are efficient in protecting neonatal calves from RVA diarrhea; however, the value of this intervention in calves once diarrhea has appeared is unclear. The aim of the present study was to evaluate the application of RVA-specific IgY as a passive treatment in those cases. The experimental groups were: G1 = RVA-specific IgY treatment; G2 = no Ab treatment; and G3 = colostrum deprived + no Ab treatment. IgY treatment significantly reduced virus shedding, diarrhea duration and severity compared to G2 and G3 calves. However, it caused a partial suppression of systemic Ab responses to RVA that could be associated with less severe diarrhea. The oral treatment with IgY for 7 days was associated with significantly higher antibody secreting cell responses in the calves compared with other groups of animals.

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Neonatal calf diarrhea is a critical problem and passive therapy with IgY Abs is a way to control it.

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There are no solid studies using rotavirus specific IgY Abs once calves suffer from diarrhea.

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We provide here scientific information regarding the effects of IgY-based products.

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This information is critical considering that IgY Abs are being sold in several countries.

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We prove the therapeutic value of IgY-based treatment and the industrialization of this product.

The mold integration method for the calculation of the crystal-fluid interfacial free energy from simulations

The interfacial free energy between a crystal and a fluid, γcf, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring γcf experimentally, computer simulations are often used to study the crystal-fluid interface. Here, we present a novel simulation methodology for the calculation of γcf. The methodology consists in using a mold composed of potential energy wells to induce the formation of a crystal slab in the fluid at coexistence conditions. This induction is done along a reversible pathway along which the free energy difference between the initial and the final states is obtained by means of thermodynamic integration. The structure of the mold is given by that of the crystal lattice planes, which allows to easily obtain the free energy for different crystal orientations. The method is validated by calculating γcf for previously studied systems, namely, the hard spheres and the Lennard-Jones systems. Our results for the latter show that the method is accurate enough to deal with the anisotropy of γcf with respect to the crystal orientation. We also calculate γcf for a recently proposed continuous version of the hard sphere potential and obtain the same γcf as for the pure hard sphere system. The method can be implemented both in Monte Carlo and Molecular Dynamics. In fact, we show that it can be easily used in combination with the popular Molecular Dynamics package GROMACS.

Free energy calculations for molecular solids using GROMACS

In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.

Évaluation de l’intérêt d’un Serious game chez des patients souffrant de troubles bipolaires inclus dans un programme de psychoéducation

Introduction

La psychoéducation du trouble bipolaire favorise l’adhésion thérapeutique et le maintien de l’euthymie à 2 ans [1]. Au terme d’un tel programme, les patients peuvent avoir besoin d’aide pour perpétuer la mise en place des apprentissages concernant l’observance thérapeutique, les routines de vie quotidienne, l’évitement des toxiques et le repérage des prodromes thymiques. Le Serious Game BIPOLIFE®, jeu centré sur un avatar souffrant de trouble bipolaire évoluant dans des situations de la vie courante, s’articule aussi autour de ces cibles.

Objectifs

Évaluer la qualité de l’observance thérapeutique par la Medication Adherence Rating Scale (MARS) [2], les indicateurs de routine de vie et de recours aux soins psychiatriques à 1 et 4 mois de la dernière séance de psychoéducation chez les patients utilisant BIPOLIFE® vs. suivi habituel.

Méthodologie

Étude pilote multicentrique randomisée contrôlée à 2 bras (durée : 24 mois) incluant des sujets euthymiques (score de dépression MADRS ≤ 12 et de manie YMRS ≤ 8 depuis 3 mois), bénéficiant d’un programme de psychoéducation. Les patients du groupe « intervention » se connecteront au site BIPOLIFE®, de manière hebdomadaire, pendant un mois (durée de connexion libre). À l’inclusion (dernière séance de psychoéducation), 1 et 4 mois, seront évalués l’attitude vis-à-vis du traitement, la qualité du sommeil, l’indice de masse corporelle, le périmètre ombilical, la consommation de toxiques, le fonctionnement psychosocial et le recours aux soins psychiatriques.

Perspectives

Proposer BIPOLIFE® en add-on de la psychoéducation pour renforcer les compétences acquises lors du programme et le maintien de l’euthymie.

Fluid-solid equilibrium of carbon dioxide as obtained from computer simulations of several popular potential models: the role of the quadrupole

In this work the solid-fluid equilibrium for carbon dioxide (CO2) has been evaluated using Monte Carlo simulations. In particular the melting curve of the solid phase denoted as I, or dry ice, was computed for pressures up to 1000 MPa. Four different models, widely used in computer simulations of CO2 were considered in the calculations. All of them are rigid non-polarizable models consisting of three Lennard-Jones interaction sites located on the positions of the atoms of the molecule, plus three partial charges. It will be shown that although these models predict similar vapor-liquid equilibria their predictions for the fluid-solid equilibria are quite different. Thus the prediction of the entire phase diagram is a severe test for any potential model. It has been found that the Transferable Potentials for Phase Equilibria (TraPPE) model yields the best description of the triple point properties and melting curve of carbon dioxide. It is shown that the ability of a certain model to predict the melting curve of carbon dioxide is related to the value of the quadrupole moment of the model. Models with low quadrupole moment tend to yield melting temperatures too low, whereas the model with the highest quadrupole moment yields the best predictions. That reinforces the idea that not only is the quadrupole needed to provide a reasonable description of the properties in the fluid phase, but also it is absolutely necessary to describe the properties of the solid phase.