Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2.

From the perspectives of molecular biology, genetics and biothermodynamics, SARS-CoV-2 is the among the best characterized viruses. Research on SARS-CoV-2 has shed a new light onto driving forces and molecular mechanisms of viral evolution. This paper reports results on empirical formulas, biosynthesis reactions and thermodynamic properties of biosynthesis (multiplication) for the Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. Thermodynamic analysis has shown that the physical driving forces for evolution of SARS-CoV-2 are Gibbs energy of biosynthesis and Gibbs energy of binding. The driving forces have led SARS-CoV-2 through the evolution process from the original Hu-1 to the newest variants in accordance with the expectations of the evolution theory.

SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants.

SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.

Interaction of GC376, a SARS-COV-2 MPRO inhibitor, with model lipid membranes

Partitioning and effect of antiviral GC376, a potential SARS-CoV-2 inhibitor, on model lipid membranes was studied using dynamic light scattering (DLS), UV–VIS spectrometry, Excimer fluorescence, Differential scanning calorimetry (DSC) and Small- and Wide-angle X-ray scattering (SAXS/WAXS). Partition coefficient of GC376 between lipid and water phase was found to be low, reaching KP = 46.8 ± 18.2. Results suggest that GC376 partitions into lipid bilayers at the level of lipid head-groups, close to the polar/hydrophobic interface. Changes in structural and thermodynamic properties strongly depend on the GC376/lipid mole ratio. Already at lowest mole ratios GC376 induces increase of lateral pressures, mainly in the interfacial region of the bilayer. Hereby, the pre- and main-transition temperature of the lipid system increases, what is attributed to tighter packing of acyl chains induced by GC376. At GC376/DPPC ≥ 0.03 mol/mol we detected formation of domains with different GC376 content resulting in the lateral phase separation and changes in both, main transition temperature and enthalpy. The observed changes are attributed to the response of the system on the increased lateral stresses induced by partitioning of GC376. Obtained results are discussed in context of liposome-based drug delivery systems for GC376 and in context of indirect mechanism of virus replication inhibition.

Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022).

Biothermodynamics of viruses is among the youngest but most rapidly developing scientific disciplines. During the COVID-19 pandemic, it closely followed the results published by molecular biologists. Empirical formulas were published for 50 viruses and thermodynamic properties for multiple viruses and virus variants, including all variants of concern of SARS-CoV-2, SARS-CoV, MERS-CoV, Ebola virus, Vaccinia and Monkeypox virus. A review of the development of biothermodynamics of viruses during the last several decades and intense development during the last 3 years is described in this paper.

Microwave treatment to optimize physicochemical properties of modified Busil (Xanthosoma sagittifolium) starch

COVID-19 pandemic encourages the utilization of local food sources to ensure food availability. Busil (Xanthosoma sagittifolium) was readily available and affordable in Banjarnegara Regency in the Province of Central Java in Indonesia. However, the busil starch utilization was still rare due to the low functional properties of the native busil starch. The objective of this study was to explore busil starch physicochemical characterization enhancement after microwave irradiation treatment, especially on the stability of heat processing. This research was conducted in two steps. First, microwave treatment (with a variation of energy and irradiation time) of native busil starch (NBS), and the second was modified busil starch (MBS) physicochemical characterization. A rise in amylose was observed on MBS. SEM analysis was shown MBS granules are breakdown. Through viscosity, final viscosity, setback viscosity, peak time, and the pasting temperature of MBS generally were increased. Meanwhile, peak viscosity and breakdown viscosity of MBS was decreased. Thermal properties of MBS like onset (To), peak (Tp), and conclusion (Tc) temperatures were also increased. The degree of whiteness index (DW) of MBS was decreased. FTIR analysis has shown that microwave treatment did not cause functional group alteration. XRD analysis has also demonstrated no change in the diffraction pattern but a slight change in the crystallinity index. Generally, microwave treatment leads to MBS thermal stability and potentially broaden MBS utilization on food processing product.

Polymer Membranes for Enthalpy Exchangers

A membrane-based enthalpy exchanger is a device used for heat and humidity recovery in ventilated buildings. The energy-saving potential of such a device is dependent on the parameters responsible for heat and moisture recovery. The trend is toward composite membranes, which are custom produced, and their parameters can be adjusted for a given application;therefore, the diffusion and sorption characteristics of such membranes are unknown. In order to obtain the values of the water vapor diffusivity of three investigated handmade membranes, a serial resistance model using a Field and Laboratory Emission Cell (FLEC) is proposed. Experiments were conducted to identify the resistance in each step of the moisture transfer process to extract the moisture diffusivity in the membranes. The calculated moisture diffusivities in the membranes were 8.99 × 10−12 (m2/s) for the membranes from cellulose acetate, 1.9 × 10−10 (m2/s) for the microporous PE/PUR membranes, and 1.53 × 10−11 (m2/s) for the PET/PUR microfibrous membranes. The obtained membrane diffusivities were then used in the proposed effectiveness-NTU-based model of an exchanger with a cross-flow arrangement to predict performance under various operating conditions. The results show that the highest latent effectiveness was found for the exchanger core made from the PE/PUR membrane and the lowest was for the one with the PE/PUR membrane core.

Ve-Degree, Ev-Degree, and Degree-Based Topological Indices of Fenofibrate

The molecular topology of a graph is described by topological indices, which are numerical measures. In theoretical chemistry, topological indices are numerical quantities that are used to represent the molecular topology of networks. These topological indices can be used to calculate several physical and chemical properties of chemical compounds, such as boiling point, entropy, heat generation, and vaporization enthalpy. Graph theory comes in handy when looking at the link between certain topological indices of some derived graphs. In the ongoing research, we determine ve-degree, ev-degree, and degree-based (D-based) topological indices of fenofibrate’s chemical structure. These topological indices are the Zagreb index, general Randić index, modified Zagreb index, and forgotten topological index. These indices are very helpful to study the characterization of the given structure.

Strain wars 4 - Darwinian evolution through Gibbs' glasses: Gibbs energies of binding and growth explain evolution of SARS-CoV-2 from Hu-1 to BA.2.

All processes in nature are driven by negative Gibbs energy. Gibbs energy is used by various viruses and their strains to hijack host cell metabolic machinery. The analysis was made by using the atom counting method to obtain elemental compositions and Gibbs energy of growth of the BA.2 strain of SARS-CoV-2. Moreover, Gibbs energy of binding was determined for the BA.2 strain. The properties of BA.2 were compared to those of Hu-1, Delta and Omicron strains. It is concluded that SARS-CoV-2 has evolved by making its Gibbs energy of binding more negative. Hence, it seems that the change in Gibbs energy of binding plays the major role in SARS-CoV-2 evolution. Therefore, Gibbs energy difference between various strains represents the possible mechanism of Darwinian evolution of viruses. In particular, a virus evolves through mutations, resulting in change in information content, elemental composition, increase in infectivity and decrease in pathogenicity.

Studying Kinetic and Thermodynamic Parameters of the Interaction of Ceftriaxone with Albumin Extracted from Healthy and Covid-19 Plasma

Because it has been well defined, bovine serum albumin (BSA) is highly suited to pharmacological effects, biotransformation, and bio-distribution of medicines initial research. Drug–protein interactions in the blood stream are known to have a significant impact on drug distribution, free concentration, and metabolism. Coronavirus disease 2019 (COVID-19) has spread globally as a severe pandemic. It is a serious threat to healthcare systems, economies, and is devastating to some populations, such as the elderly and those with comorbidities. Unfortunately, there is still no effective cure for COVID-19, especially the critically ill patients. The link between the mortality risk of patients hospitalized for COVID-19 and the function of blood albumin levels has been investigated. Because of albumin biological significance, the study goal conducted to apply spectroscopic methods to explore and comparing the kinetic and thermodynamic aspects of ceftriaxone's interaction with BSA, albumin isolated from healthy and covid-19 plasma. A pooled plasma from healthy and hospitalized covid-19 individuals (Karbala Province / Iraq) was used to purify albumin using HPLC technique. UV-vis spectrophotometric measurements of albumin-ceftriaxone complex formation recorded at different pH (7, 7.2, 7.4, 7.6 & 7.8) in phosphate buffer solution, and at six different temperatures (298, 301, 304, 307, 310 & 313) K. The equilibrium constant and the thermodynamic parameter such as ΔG, ΔH and ΔS were calculated. The drug-albumin (BSA, healthy and Covid-19 albumin) complexes are stable in 60 to 300 minutes, as evidenced by the steady absorbance studies. The reaction is from the first false order for drug-albumin (BSA, healthy and covid-19 plasma) complexes. Our finding suggesting the reaction is from the first false order. In the case of plasma albumin from individuals infected with - Covid-19, the values of (R2) are closer together. This is because the medication dominates the formation of a more stable complex with albumin. The stoichiometric ratio (coordination number) of complex between ceftriaxone and albumin at 298 k and pH=7.4 is 1:1. The Gibbs free energy for albumin-ceftriaxone is negative, indicating that the reaction is spontaneous. The positive enthalpy of contact indicates that the process is endothermic, requiring energy input. Positive enthalpy and entropy change also refer to the hydrophobic association and electrostatic contact that occurs between albumin molecules and ceftriaxone. It is worth noting that the complex formed between bovine albumin and the medication has less absorbency at pH = 7.4. That is, the complex is more stable, and it prefers natural helical shapes. Additionally, as the pH value shifts away from physiological (> 7.4 <), the intensity of complex absorption increases.

QSPR Modeling with Topological Indices of Some Potential Drug Candidates against COVID-19

COVID-19, which has spread all over the world and was declared as a pandemic, is a new disease caused by the coronavirus family. There is no medicine yet to prevent or end this pandemic. Even if existing drugs are used to alleviate the pandemic, this is not enough. Therefore, combinations of existing drugs and their analogs are being studied. Vaccines produced for COVID-19 may not be effective for new variants of this virus. Therefore, it is necessary to find the drugs for this disease as soon as possible. Topological indices are the numerical descriptors of a molecular structure obtained by the molecular graph. Topological indices can provide information about the physicochemical properties and biological properties of molecules in the quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR) studies. In this paper, some analogs of lopinavir, favipiravir, and ritonavir drugs that have the property of being potential drugs against COVID-19 are studied. QSPR models are studied using linear and quadratic regression analysis with topological indices for enthalpy of vaporization, flash point, molar refractivity, polarizability, surface tension, and molar volume properties of these analogs.

The Marsili Seamount Offshore Geothermal Reservoir: A Big Challenge for an Energy Transition Model

Renewable energies have been the only sources recording a clear increase in total installed capacity, setting a record in new power capacity in 2020, despite the pandemic. The European Union Green Deal represents a strategy towards a sustainable economic model. In this framework, land-based geothermics has seen very limited development;however, offshore geothermics is almost completely absent in the discussion on energy source alternatives, even though it represents a real challenge for energy transition, including the production of green hydrogen. This article discusses an excursus on the activities carried out on offshore geothermal areas worldwide. We focused on the energy potential capacity of the Marsili volcanic seamount located over the bathial plain of the Tyrrhenian Basin, describing the detailed geological, geochemical, and geophysical investigations that have been carried out on that seamount since the 2000s. All the collected data have shown evidence supporting the existence of an exploitable geothermal system in the Marsili seamount consisting of a reservoir of supercritical geothermal fluids of about 100 km3. We discuss and evaluate the actual consistence of the impacts associated with the occurrence of potential risks. We also describe the necessary further steps towards the pilot well. An important breakthrough in the short-medium term that allows for an exit from the predominance of fossil sources may come from the development of energy production derived from offshore high-enthalpy geothermal fields, especially in areas such as the Southern Tyrrhenian Sea. There is a natural clear predisposition for its exploitation combined with a low ecological footprint, which is the target objective of international agreements in the context of a blue economy strategy.

Capturing a Crucial 'Disorder-to-Order Transition' at the Heart of the Coronavirus Molecular Pathology-Triggered by Highly Persistent, Interchangeable Salt-Bridges.

The COVID-19 origin debate has greatly been influenced by genome comparison studies of late, revealing the emergence of the Furin-like cleavage site at the S1/S2 junction of the SARS-CoV-2 Spike (FLCSSpike) containing its 681PRRAR685 motif, absent in other related respiratory viruses. Being the rate-limiting (i.e., the slowest) step, the host Furin cleavage is instrumental in the abrupt increase in transmissibility in COVID-19, compared to earlier onsets of respiratory viral diseases. In such a context, the current paper entraps a 'disorder-to-order transition' of the FLCSSpike (concomitant to an entropy arrest) upon binding to Furin. The interaction clearly seems to be optimized for a more efficient proteolytic cleavage in SARS-CoV-2. The study further shows the formation of dynamically interchangeable and persistent networks of salt-bridges at the Spike-Furin interface in SARS-CoV-2 involving the three arginines (R682, R683, R685) of the FLCSSpike with several anionic residues (E230, E236, D259, D264, D306) coming from Furin, strategically distributed around its catalytic triad. Multiplicity and structural degeneracy of plausible salt-bridge network archetypes seem to be the other key characteristic features of the Spike-Furin binding in SARS-CoV-2, allowing the system to breathe-a trademark of protein disorder transitions. Interestingly, with respect to the homologous interaction in SARS-CoV (2002/2003) taken as a baseline, the Spike-Furin binding events, generally, in the coronavirus lineage, seems to have preference for ionic bond formation, even with a lesser number of cationic residues at their potentially polybasic FLCSSpike patches. The interaction energies are suggestive of characteristic metastabilities attributed to Spike-Furin interactions, generally to the coronavirus lineage, which appears to be favorable for proteolytic cleavages targeted at flexible protein loops. The current findings not only offer novel mechanistic insights into the coronavirus molecular pathology and evolution, but also add substantially to the existing theories of proteolytic cleavages.

Application of Docking and Quantum Chemistry to the Search for Inhibitors of SARS-CoV-2 Main Protease

Docking and quantum-chemical molecular modeling methods have been applied to search inhibitors of the main protease of SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic. More than 14 thousand organic compounds from the commercially available Maybridge database were docked into the active site of main protease using the SOL docking program, and more than 100 ligands with the most negative SOL scores were selected for further processing. For all these top scored ligands, the enthalpy of protein-ligand binding was calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. When calculating the enthalpy of protein-ligand binding, a best docked ligand pose was used as the initial conformation for local energy optimization by the PM7 method with varying the positions of all ligand atoms. In the optimized ligand pose, the energy of the protein-ligand complex was recalculated with the COSMO solvent for fixed positions of all atoms of the system. For further experimental testing, 18 ligands were selected with the following criteria: good SOL scores, the most negative binding enthalpies, favorable protein-ligand interactions inferred from visual inspection of the docking poses and chemical diversity of the ligands. The selected ligands are planned to be measured in vitro for their inhibition of the main protease SARS-CoV-2. In the case of experimental confirmation of their inhibitory activity, these compounds can be used to further optimize their chemical structure in order to obtain a lead compound – the basis for new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus. © 2021, Springer Nature Switzerland AG.

Direct solar vapor generation with micro‐3D printed hydrogel device

Direct solar vapor generation (SVG) provides a sustainable and eco‐friendly solution to the current global water scarcity challenges. However, existing SVG systems operating under natural sunlight suffer from low water yield and high energy requirement of vaporization. New materials with reduced latent heat of water vaporization are in urgent demand to boost SVG process. Herein, we propose a novel strategy to additively fabricate anisotropic hybrid 3D structure from photocurable thermoresponsive p(NIPAm‐co‐PEGDA) hydrogel on the top of PEGDA foam for SVG. The in‐situ post‐printing synthesis of iron oxide nanoparticles within the p(NIPAm‐co‐PEGDA) hydrogel on the top surface, thus introducing anisotropy, is achieved by adding metallic salt precursor into the printing solution. The as‐fabricated hydrogel composite structure exhibits superior light absorption properties and rapid capillary‐driven water transport through a 3D‐printed microchannel network within the hydrogel. As a result, our SVG device achieves an extraordinary water evaporation rate of 5.12 kg m−2 h−1 under one sun (1 kW/m2). The intrinsic water activation states, in addition to wettability modulation with temperature increase within p(NIPAm‐co‐PEGDA) hydrogel, plays a critical role in reducing the equivalent vaporization enthalpy and shifting the vaporization to relatively lower temperatures. The proposed hybrid SVG device is feasible, portable, and highly efficient, promising great potential for grand water‐energy nexus challenges.

Predicting SARS-CoV-2 Weather-Induced Seasonal Virulence from Atmospheric Air Enthalpy.

Following the coronavirus disease 2019 (COVID-19) pandemic, several studies have examined the possibility of correlating the virulence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, to the climatic conditions of the involved sites; however, inconclusive results have been generally obtained. Although neither air temperature nor humidity can be independently correlated with virus viability, a strong relationship between SARS-CoV-2 virulence and the specific enthalpy of moist air appears to exist, as confirmed by extensive data analysis. Given this framework, the present study involves a detailed investigation based on the first 20-30 days of the epidemic before public health interventions in 30 selected Italian provinces with rather different climates, here assumed as being representative of what happened in the country from North to South, of the relationship between COVID-19 distributions and the climatic conditions recorded at each site before the pandemic outbreak. Accordingly, a correlating equation between the incidence rate at the early stage of the epidemic and the foregoing average specific enthalpy of atmospheric air was developed, and an enthalpy-based seasonal virulence risk scale was proposed to predict the potential danger of COVID-19 outbreak due to the persistence of weather conditions favorable to SARS-CoV-2 viability. As an early detection tool, an unambiguous risk chart expressed in terms of coupled temperatures and relative humidity (RH) values was provided, showing that safer conditions occur in the case of higher RHs at the highest temperatures, and of lower RHs at the lowest temperatures. Despite the complex determinism and dynamics of the pandemic and the related caveats, the restriction of the study to its early stage allowed the proposed risk scale to result in agreement with the available infectivity data highlighted in the literature for a number of cities around the world.

Performance analysis of a hybrid ventilation system in a near zero energy building.

In this research paper, an analysis is developed on the performance of a hybrid ventilation system that combines Earth-to-Air Heat eXchangers (EAHX), free cooling and evaporative cooling Air Handling Unit Heat eXchanger (AHU-HX), all being controlled by a Building Management System (BMS) in a net Zero Energy Building (nZEB), called LUCIA. LUCIA nZEB is the first safe-building against Covid-19 in the world, certified by the international organisation WOSHIE, and located in Valladolid, Spain. The main aim is to optimize the performance of the three systems in such a way that the Indoor Air Quality (IAQ) levels remain within the allowable limits, while maximizing the use of natural resources and minimizing energy consumption and carbon emissions. The approach to satisfy the heating and cooling demand and IAQ levels through zero emissions energy systems is developed, thus anticipating the zero-energy target, set by the European Union for 2050. Results showed that the installed hybrid ventilation system uses heat exchangers for 70% of the operational time, in order to achieve the set parameters successfully. Also, the analysis made by monitoring data, have shown that the control and optimal operation of the hybrid ventilation system allows high energy recovery values with minimum additional electricity consumption. Significant reduction of carbon emissions and operational costs have been achieved.

On the Optimal Indoor Air Conditions for SARS-CoV-2 Inactivation. An Enthalpy-Based Approach.

In the CoViD-19 pandemic, the precautionary approach suggests that all possible measures should be established and implemented to avoid contagion, including through aerosols. For indoor spaces, the virulence of SARS-CoV-2 could be mitigated not only via air changes, but also by heating, ventilation, and air conditioning (HVAC) systems maintaining thermodynamic conditions possibly adverse to the virus. However, data available in literature on virus survival were never treated aiming to this. In fact, based on comparisons in terms of specific enthalpy, a domain of indoor comfort conditions between 50 and 60 kJ/kg is found to comply with this objective, and an easy-to-use relationship for setting viable pairs of humidity and temperature using a proper HVAC plant is proposed. If confirmed via further investigations on this research path, these findings could open interesting scenarios on the use of indoor spaces during the pandemic.