Otto Engine for the q-State Clock Model.

This present work explores the performance of a thermal-magnetic engine of Otto type, considering as a working substance an effective interacting spin model corresponding to the q- state clock model. We obtain all the thermodynamic quantities for the q = 2, 4, 6, and 8 cases in a small lattice size (3×3 with free boundary conditions) by using the exact partition function calculated from the energies of all the accessible microstates of the system. The extension to bigger lattices was performed using the mean-field approximation. Our results indicate that the total work extraction of the cycle is highest for the q=4 case, while the performance for the Ising model (q=2) is the lowest of all cases studied. These results are strongly linked with the phase diagram of the working substance and the location of the cycle in the different magnetic phases present, where we find that the transition from a ferromagnetic to a paramagnetic phase extracts more work than one of the Berezinskii-Kosterlitz-Thouless to paramagnetic type. Additionally, as the size of the lattice increases, the extraction work is lower than smaller lattices for all values of q presented in this study.

Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces.

The COVID-19 pandemic has claimed millions of lives worldwide, sickened many more, and has resulted in severe socioeconomic consequences. As society returns to normal, understanding the spread and persistence of SARS CoV-2 on commonplace surfaces can help to mitigate future outbreaks of coronaviruses and other pathogens. We hypothesize that such an understanding can be aided by studying the binding and interaction of viral proteins with nonbiological surfaces. Here, we propose a methodology for investigating the adhesion of the SARS CoV-2 spike glycoprotein on common inorganic surfaces such as aluminum, copper, iron, silica, and ceria oxides as well as metallic gold. Quantitative adhesion was obtained from the analysis of measured forces at the nanoscale using an atomic force microscope operated under ambient conditions. Without imposing further constraints on the measurement conditions, our preliminary findings suggest that spike glycoproteins interact with similar adhesion forces across the majority of the metal oxides tested with the exception to gold, for which attraction forces ∼10 times stronger than all other materials studied were observed. Ferritin, which was used as a reference protein, was found to exhibit similar adhesion forces as SARS CoV-2 spike protein. This study results show that glycoprotein adhesion forces for similar ambient humidity, tip shape, and contact surface are nonspecific to the properties of metal oxide surfaces, which are expected to be covered by a thin water film. The findings suggest that under ambient conditions, glycoprotein adhesion to metal oxides is primarily controlled by the water capillary forces, and they depend on the surface tension of the liquid water. We discuss further strategies warranted to decipher the intricate nanoscale forces for improved quantification of the adhesion.

Short-Range Berezinskii-Kosterlitz-Thouless Phase Characterization for the q-State Clock Model.

Beyond the usual ferromagnetic and paramagnetic phases present in spin systems, the usual q-state clock model presents an intermediate vortex state when the number of possible orientations q for the system is greater than or equal to 5. Such vortex states give rise to the Berezinskii-Kosterlitz-Thouless (BKT) phase present up to the XY model in the limit q→∞. Based on information theory, we present here an analysis of the classical order parameters plus new short-range parameters defined here. Thus, we show that even using the first nearest neighbors spin-spin correlations only, it is possible to distinguish the two transitions presented by this system for q greater than or equal to 5. Moreover, the appearance at relatively low temperature and disappearance of the BKT phase at a rather fix higher temperature is univocally determined by the short-range interactions recognized by the information content of classical and new parameters.

Otto Engine: Classical and Quantum Approach.

In this paper, we analyze the total work extracted and the efficiency of the magnetic Otto cycle in its classic and quantum versions. As a general result, we found that the work and efficiency of the classical engine is always greater than or equal to its quantum counterpart, independent of the working substance. In the classical case, this is due to the fact that the working substance is always in thermodynamic equilibrium at each point of the cycle, maximizing the energy extracted in the adiabatic paths. We apply this analysis to the case of a two-level system, finding that the work and efficiency in both the Otto's quantum and classical cycles are identical, regardless of the working substance, and we obtain similar results for a multilevel system where a linear relationship between the spectrum of energies of the working substance and the external magnetic field is fulfilled. Finally, we show an example of a three-level system in which we compare two zones in the entropy diagram as a function of temperature and magnetic field to find which is the most efficient region when performing a thermodynamic cycle. This work provides a practical way to look for temperature and magnetic field zones in the entropy diagram that can maximize the power extracted from an Otto magnetic engine.

Magnetic Otto Engine for an Electron in a Quantum Dot: Classical and Quantum Approach.

We studied the performance of classical and quantum magnetic Otto cycle with a working substance composed of a single quantum dot using the Fock-Darwin model with the inclusion of the Zeeman interaction. Modulating an external/perpendicular magnetic field, in the classical approach, we found an oscillating behavior in the total work extracted that was not present in the quantum formulation.We found that, in the classical approach, the engine yielded a greater performance in terms of total work extracted and efficiency than when compared with the quantum approach. This is because, in the classical case, the working substance can be in thermal equilibrium at each point of the cycle, which maximizes the energy extracted in the adiabatic strokes.

Magnetocaloric Effect in Non-Interactive Electron Systems: "The Landau Problem" and Its Extension to Quantum Dots.

In this work, we report the magnetocaloric effect (MCE) in two systems of non-interactive particles: the first corresponds to the Landau problem case and the second the case of an electron in a quantum dot subjected to a parabolic confinement potential. In the first scenario, we realize that the effect is totally different from what happens when the degeneracy of a single electron confined in a magnetic field is not taken into account. In particular, when the degeneracy of the system is negligible, the magnetocaloric effect cools the system, while in the other case, when the degeneracy is strong, the system heats up. For the second case, we study the competition between the characteristic frequency of the potential trap and the cyclotron frequency to find the optimal region that maximizes the ΔT of the magnetocaloric effect, and due to the strong degeneracy of this problem, the results are in coherence with those obtained for the Landau problem. Finally, we consider the case of a transition from a normal MCE to an inverse one and back to normal as a function of temperature. This is due to the competition between the diamagnetic and paramagnetic response when the electron spin in the formulation is included.

Magnetocaloric Effect in an Antidot: The Effect of the Aharonov-Bohm Flux and Antidot Radius.

In this work, we report the magnetocaloric effect (MCE) for an electron interacting with an antidot, under the effect of an Aharonov-Bohm flux (AB-flux) subjected to a parabolic confinement potential. We use the Bogachek and Landman model, which additionally allows the study of quantum dots with Fock-Darwin energy levels for vanishing antidot radius and AB-flux. We find that AB-flux strongly controls the oscillatory behaviour of the MCE, thus acting as a control parameter for the cooling or heating of the magnetocaloric effect. We propose a way to detect AB-flux by measuring temperature differences.

Entropy and Mutability for the q-State Clock Model in Small Systems.

In this paper, we revisit the q-state clock model for small systems. We present results for the thermodynamics of the q-state clock model for values from q = 2 to q = 20 for small square lattices of L × L , with L ranging from L = 3 to L = 64 with free-boundary conditions. Energy, specific heat, entropy, and magnetization were measured. We found that the Berezinskii-Kosterlitz-Thouless (BKT)-like transition appears for q > 5, regardless of lattice size, while this transition at q = 5 is lost for L < 10; for q ≤ 4, the BKT transition is never present. We present the phase diagram in terms of q that shows the transition from the ferromagnetic (FM) to the paramagnetic (PM) phases at the critical temperature T 1 for small systems, and the transition changes such that it is from the FM to the BKT phase for larger systems, while a second phase transition between the BKT and the PM phases occurs at T 2. We also show that the magnetic phases are well characterized by the two-dimensional (2D) distribution of the magnetization values. We made use of this opportunity to carry out an information theory analysis of the time series obtained from Monte Carlo simulations. In particular, we calculated the phenomenological mutability and diversity functions. Diversity characterizes the phase transitions, but the phases are less detectable as q increases. Free boundary conditions were used to better mimic the reality of small systems (far from any thermodynamic limit). The role of size is discussed.

A Genome-Wide RNA Interference Screen Identifies a Role for Wnt/ß-Catenin Signaling during Rift Valley Fever Virus Infection.

UNLABELLED: Rift Valley fever virus (RVFV) is an arbovirus within the Bunyaviridae family capable of causing serious morbidity and mortality in humans and livestock. To identify host factors involved in bunyavirus replication, we employed genome-wide RNA interference (RNAi) screening and identified 381 genes whose knockdown reduced infection. The Wnt pathway was the most represented pathway when gene hits were functionally clustered. With further investigation, we found that RVFV infection activated Wnt signaling, was enhanced when Wnt signaling was preactivated, was reduced with knockdown of ß-catenin, and was blocked using Wnt signaling inhibitors. Similar results were found using distantly related bunyaviruses La Crosse virus and California encephalitis virus, suggesting a conserved role for Wnt signaling in bunyaviral infection. We propose a model where bunyaviruses activate Wnt-responsive genes to regulate optimal cell cycle conditions needed to promote efficient viral replication. The findings in this study should aid in the design of efficacious host-directed antiviral therapeutics. IMPORTANCE: RVFV is a mosquito-borne bunyavirus that is endemic to Africa but has demonstrated a capacity for emergence in new territories (e.g., the Arabian Peninsula). As a zoonotic pathogen that primarily affects livestock, RVFV can also cause lethal hemorrhagic fever and encephalitis in humans. Currently, there are no treatments or fully licensed vaccines for this virus. Using high-throughput RNAi screening, we identified canonical Wnt signaling as an important host pathway regulating RVFV infection. The beneficial role of Wnt signaling was observed for RVFV, along with other disparate bunyaviruses, indicating a conserved bunyaviral replication mechanism involving Wnt signaling. These studies supplement our knowledge of the fundamental mechanisms of bunyavirus infection and provide new avenues for countermeasure development against pathogenic bunyaviruses.

Identification of critical amino acids within the nucleoprotein of Tacaribe virus important for anti-interferon activity.

The arenavirus nucleoprotein (NP) can suppress induction of type I interferon (IFN). This anti-IFN activity is thought to be shared by all arenaviruses with the exception of Tacaribe virus (TCRV). To identify the TCRV NP amino acid residues that prevent its IFN-countering ability, we created a series of NP chimeras between residues of TCRV NP and Pichinde virus (PICV) NP, an arenavirus NP with potent anti-IFN function. Chimera NP analysis revealed that a minimal four amino acid stretch derived from PICV NP could impart efficient anti-IFN activity to TCRV NP. Strikingly, the TCRV NP gene cloned and sequenced from viral stocks obtained through National Institutes of Health Biodefense and Emerging Infections (BEI) resources deviated from the reference sequence at this particular four-amino acid region, GPPT (GenBank KC329849) versus DLQL (GenBank NC004293), respectively at residues 389-392. When efficiently expressed in cells through codon-optimization, TCRV NP containing the GPPT residues rescued the antagonistic IFN function. Consistent with cell expression results, TCRV infection did not stimulate an IFNß response early in infection in multiple cells types (e.g. A549, P388D1), and IRF-3 was not translocated to the nucleus in TCRV-infected A549 cells. Collectively, these data suggest that certain TCRV strain variants contain the important NP amino acids necessary for anti-IFN activity.

Cysteines in the stalk of the nipah virus G glycoprotein are located in a distinct subdomain critical for fusion activation.

Paramyxoviruses initiate entry through the concerted action of the tetrameric attachment glycoprotein (HN, H, or G) and the trimeric fusion glycoprotein (F). The ectodomains of HN/H/G contain a stalk region important for oligomeric stability and for the F triggering resulting in membrane fusion. Paramyxovirus HN, H, and G form a dimer-of-dimers consisting of disulfide-linked dimers through their stalk domain cysteines. The G attachment protein stalk domain of the highly pathogenic Nipah virus (NiV) contains a distinct but uncharacterized cluster of three cysteine residues (C146, C158, C162). On the basis of a panoply of assays, we report that C158 and C162 of NiV-G likely mediate covalent subunit dimerization, while C146 mediates the stability of higher-order oligomers. For HN or H, mutation of stalk cysteines attenuates but does not abrogate the ability to trigger fusion. In contrast, the NiV-G stalk cysteine mutants were completely deficient in triggering fusion, even though they could still bind the ephrinB2 receptor and associate with F. Interestingly, all cysteine stalk mutants exhibited constitutive exposure of the Mab45 receptor binding-enhanced epitope, previously implicated in F triggering. The enhanced binding of Mab45 to the cysteine mutants relative to wild-type NiV-G, without the addition of the receptor, implicates the stalk cysteines in the stabilization of a pre-receptor-bound conformation and the regulation of F triggering. Sequence alignments revealed that the stalk cysteines were adjacent to a proline-rich microdomain unique to the Henipavirus genus. Our data propose that the cysteine cluster in the NiV-G stalk functions to maintain oligomeric stability but is more importantly involved in stabilizing a unique microdomain critical for triggering fusion.

Rift Valley fever virus strain MP-12 enters mammalian host cells via caveola-mediated endocytosis.

Rift Valley fever virus (RVFV) is a zoonotic pathogen capable of causing serious morbidity and mortality in both humans and livestock. The lack of efficient countermeasure strategies, the potential for dispersion into new regions, and the pathogenesis in humans and livestock make RVFV a serious public health concern. The receptors, cellular factors, and entry pathways used by RVFV and other members of the family Bunyaviridae remain largely uncharacterized. Here we provide evidence that RVFV strain MP-12 uses dynamin-dependent caveola-mediated endocytosis for cell entry. Caveolae are lipid raft domains composed of caveolin (the main structural component), cholesterol, and sphingolipids. Caveola-mediated endocytosis is responsible for the uptake of a wide variety of host ligands, as well as bacteria, bacterial toxins, and a number of viruses. To determine the cellular entry mechanism of RVFV, we used small-molecule inhibitors, RNA interference (RNAi), and dominant negative (DN) protein expression to inhibit the major mammalian cell endocytic pathways. Inhibitors and RNAi specific for macropinocytosis and clathrin-mediated endocytosis had no effect on RVFV infection. In contrast, inhibitors of caveola-mediated endocytosis, and RNAi targeted to caveolin-1 and dynamin, drastically reduced RVFV infection in multiple cell lines. Expression of DN caveolin-1 also reduced RVFV infection significantly, while expression of DN EPS15, a protein required for the assembly of clathrin-coated pits, and DN PAK-1, an obligate mediator of macropinocytosis, had no significant impact on RVFV infection. These results together suggest that the primary mechanism of RVFV MP-12 uptake is dynamin-dependent, caveolin-1-mediated endocytosis.

A broad-spectrum antiviral targeting entry of enveloped viruses.

We describe an antiviral small molecule, LJ001, effective against numerous enveloped viruses including Influenza A, filoviruses, poxviruses, arenaviruses, bunyaviruses, paramyxoviruses, flaviviruses, and HIV-1. In sharp contrast, the compound had no effect on the infection of nonenveloped viruses. In vitro and in vivo assays showed no overt toxicity. LJ001 specifically intercalated into viral membranes, irreversibly inactivated virions while leaving functionally intact envelope proteins, and inhibited viral entry at a step after virus binding but before virus-cell fusion. LJ001 pretreatment also prevented virus-induced mortality from Ebola and Rift Valley fever viruses. Structure-activity relationship analyses of LJ001, a rhodanine derivative, implicated both the polar and nonpolar ends of LJ001 in its antiviral activity. LJ001 specifically inhibited virus-cell but not cell-cell fusion, and further studies with lipid biosynthesis inhibitors indicated that LJ001 exploits the therapeutic window that exists between static viral membranes and biogenic cellular membranes with reparative capacity. In sum, our data reveal a class of broad-spectrum antivirals effective against enveloped viruses that target the viral lipid membrane and compromises its ability to mediate virus-cell fusion.

Future of Mesoporous Silica Nanoparticles in Nanomedicine: Protocol for Reproducible Synthesis, Characterization, Lipid Coating, and Loading of Therapeutics (Chemotherapeutic, Proteins, siRNA and mRNA).

Owing to their uniform and tunable particle size, pore size, and shape, along with their modular surface chemistry and biocompatibility, mesoporous silica nanoparticles (MSNs) have found extensive applications as nanocarriers to deliver therapeutic, diagnostic and combined "theranostic" cargos to cells and tissues. Although thoroughly investigated, MSN have garnered FDA approval for only one MSN system via oral administration. One possible reason is that there is no recognized, reproducible, and widely adopted MSN synthetic protocol, meaning not all MSNs are created equal in the laboratory nor in the eyes of the FDA. This manuscript provides the sol-gel and MSN research communities a reproducible, fully characterized synthetic protocol to synthesize MSNs and corresponding lipid-coated MSN delivery vehicles with predetermined particle size, pore size, and drug loading and release characteristics. By carefully articulating the step-by-step synthetic procedures and highlighting critical points and troubleshooting, augmented with videos and schematics, this Article will help researchers entering this rapidly expanding field to yield reliable results.

Lipid-coated mesoporous silica nanoparticles for anti-viral applications via delivery of CRISPR-Cas9 ribonucleoproteins.

Emerging and re-emerging viral pathogens present a unique challenge for anti-viral therapeutic development. Anti-viral approaches with high flexibility and rapid production times are essential for combating these high-pandemic risk viruses. CRISPR-Cas technologies have been extensively repurposed to treat a variety of diseases, with recent work expanding into potential applications against viral infections. However, delivery still presents a major challenge for these technologies. Lipid-coated mesoporous silica nanoparticles (LCMSNs) offer an attractive delivery vehicle for a variety of cargos due to their high biocompatibility, tractable synthesis, and amenability to chemical functionalization. Here, we report the use of LCMSNs to deliver CRISPR-Cas9 ribonucleoproteins (RNPs) that target the Niemann-Pick disease type C1 gene, an essential host factor required for entry of the high-pandemic risk pathogen Ebola virus, demonstrating an efficient reduction in viral infection. We further highlight successful in vivo delivery of the RNP-LCMSN platform to the mouse liver via systemic administration.

EphrinB2 is the entry receptor for Nipah virus, an emergent deadly paramyxovirus.

Nipah virus (NiV) is an emergent paramyxovirus that causes fatal encephalitis in up to 70 percent of infected patients, and there is evidence of human-to-human transmission. Endothelial syncytia, comprised of multinucleated giant-endothelial cells, are frequently found in NiV infections, and are mediated by the fusion (F) and attachment (G) envelope glycoproteins. Identification of the receptor for this virus will shed light on the pathobiology of NiV infection, and spur the rational development of effective therapeutics. Here we report that ephrinB2, the membrane-bound ligand for the EphB class of receptor tyrosine kinases (RTKs), specifically binds to the attachment (G) glycoprotein of NiV. Soluble Fc-fusion proteins of ephrinB2, but not ephrinB1, effectively block NiV fusion and entry into permissive cell types. Moreover, transfection of ephrinB2 into non-permissive cells renders them permissive for NiV fusion and entry. EphrinB2 is expressed on endothelial cells and neurons, which is consistent with the known cellular tropism for NiV. Significantly, we find that NiV-envelope-mediated infection of microvascular endothelial cells and primary cortical rat neurons is inhibited by soluble ephrinB2, but not by the related ephrinB1 protein. Cumulatively, our data show that ephrinB2 is a functional receptor for NiV.

Gate-tunable charge carrier electrocaloric effect in trilayer graphene.

The electrocaloric (EC) effect is the change in temperature and entropy of a material driven by the application of an electric field. Our tight-binding calculations linked to Fermi statistics, show that the EC effect can be produced in trilayer graphene (TLG) structures connected to a heat source, triggered by changes in the electronic density of states (DOS) at the Fermi level when external gate fields are applied on the outer graphene layers. We demonstrate that entropy changes are sensitive to the stacking arrangement in TLG systems. The AAA-stacked TLG presents an inverse EC response (cooling) regardless of the temperature value and gate field potential strength, whereas the EC effect in ABC-stacked TLG remains direct (heating) above room temperature. We reveal otherwise the TLG with Bernal-ABA stacking generates both the direct and inverse EC response within the same sample, associated with gate-dependent electronic transitions of thermally excited charge carriers from the valence band to the conduction band in the band structure. The novel charge carrier electrocaloric effect we propose in quantum layered systems may bring a wide variety of prototype van der Waals materials that could be used as versatile platforms to controlling the thermal response in nanodevices.

Immunocompromised Cas9 transgenic mice for rapid in vivo assessment of host factors involved in highly pathogenic virus infection.

Targeting host factors for anti-viral development offers several potential advantages over traditional countermeasures that include broad-spectrum activity and prevention of resistance. Characterization of host factors in animal models provides strong evidence of their involvement in disease pathogenesis, but the feasibility of performing high-throughput in vivo analyses on lists of genes is problematic. To begin addressing the challenges of screening candidate host factors in vivo, we combined advances in CRISPR-Cas9 genome editing with an immunocompromised mouse model used to study highly pathogenic viruses. Transgenic mice harboring a constitutively expressed Cas9 allele (Cas9 tg/tg ) with or without knockout of type I interferon receptors served to optimize in vivo delivery of CRISPR single-guide RNA (sgRNA) using Invivofectamine 3.0, a simple and easy-to-use lipid nanoparticle reagent. Invivofectamine 3.0-mediated liver-specific editing to remove activity of the critical Ebola virus host factor Niemann-Pick disease type C1 in an average of 74% of liver cells protected immunocompromised Cas9 tg/tg mice from lethal surrogate Ebola virus infection. We envision that immunocompromised Cas9 tg/tg mice combined with straightforward sgRNA in vivo delivery will enable efficient host factor loss-of-function screening in the liver and other organs to rapidly study their effects on viral pathogenesis and help initiate development of broad-spectrum, host-directed therapies against emerging pathogens.

Development of potent and effective synthetic SARS-CoV-2 neutralizing nanobodies.

The respiratory virus responsible for coronavirus disease 2019 (COVID-19), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected nearly every aspect of life worldwide, claiming the lives of over 3.9 million people globally, at the time of this publication. Neutralizing humanized nanobody (VHH)-based antibodies (VHH-huFc) represent a promising therapeutic intervention strategy to address the current SARS-CoV-2 pandemic and provide a powerful toolkit to address future virus outbreaks. Using a synthetic, high-diversity VHH bacteriophage library, several potent neutralizing VHH-huFc antibodies were identified and evaluated for their capacity to tightly bind to the SARS-CoV-2 receptor-binding domain, to prevent binding of SARS-CoV-2 spike (S) to the cellular receptor angiotensin-converting enzyme 2, and to neutralize viral infection. Preliminary preclinical evaluation of multiple VHH-huFc antibody candidates demonstrate that they are prophylactically and therapeutically effective in vivo against wildtype SARS-CoV-2. The identified and characterized VHH-huFc antibodies described herein represent viable candidates for further preclinical evaluation and another tool to add to our therapeutic arsenal to address the COVID-19 pandemic.

Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline.

A rapid response is necessary to contain emergent biological outbreaks before they can become pandemics. The novel coronavirus (SARS-CoV-2) that causes COVID-19 was first reported in December of 2019 in Wuhan, China and reached most corners of the globe in less than two months. In just over a year since the initial infections, COVID-19 infected almost 100 million people worldwide. Although similar to SARS-CoV and MERS-CoV, SARS-CoV-2 has resisted treatments that are effective against other coronaviruses. Crystal structures of two SARS-CoV-2 proteins, spike protein and main protease, have been reported and can serve as targets for studies in neutralizing this threat. We have employed molecular docking, molecular dynamics simulations, and machine learning to identify from a library of 26 million molecules possible candidate compounds that may attenuate or neutralize the effects of this virus. The viability of selected candidate compounds against SARS-CoV-2 was determined experimentally by biolayer interferometry and FRET-based activity protein assays along with virus-based assays. In the pseudovirus assay, imatinib and lapatinib had IC50 values below 10 µM, while candesartan cilexetil had an IC50 value of approximately 67 µM against Mpro in a FRET-based activity assay. Comparatively, candesartan cilexetil had the highest selectivity index of all compounds tested as its half-maximal cytotoxicity concentration 50 (CC50) value was the only one greater than the limit of the assay (>100 µM).