How substituents tune quantum interference in meta-OPE3 molecular junctions to control thermoelectric transport.

Quantum interference (QI) can strongly affect electric and thermoelectric properties of molecular junctions (MJs). So far, however, a limited number of experimental studies have explored the influence of QI on thermoelectric transport in MJs. To address this open point, we synthesized derivatives of meta-OPE3 with an electron-withdrawing nitro (-NO2) substituent or an electron-donating N,N-dimethyl amine (-NMe2) substituent, attached at two different positions of the central phenylene ring, and systematically studied the electrical conductance and thermopower of the corresponding gold-molecule-gold junctions. We show that (i) the electrical conductance of MJs depends weakly on the polarity of the substituents but strongly on the substitution position and (ii) MJs with the N,N-dimethyl amine group feature a higher thermopower than MJs with the nitro group. We also present calculations based on first principles, which explain these trends and show that the transport properties are highly sensitive to microscopic details in junctions, exhibiting destructive QI features.

A mathematical framework for analysing particle flow in a network with multiple pools.

In many real-world systems, the entry rate of particles into a lane is affected by the occupancy of nearby pools. For instance, in biological networks, the concentration of molecules on the side of a membrane affects the entry of particles through the membrane. To understand the behaviour of such networks, we develop a network model of ribosome flow models (RFMs) having multiple pools where each RFM captures the dynamics of particle flow in a lane and competes for the finite resources present at the nearby pool. We study a ribosome flow model network with two pools (RFMNTP) and show that the network always admits a steady state. We then analyse the behaviour of the RFMNTP with respect to modifying the transition rate through a theoretical framework. Simulations of the RFMNTP demonstrate a counterintuitive result. For example, increasing any of the transition rates in the presence of a slow site in an RFM can increase the output rate of some RFMs and decrease the output rate of the other RFMs simultaneously. This suggests that the role of local sharing of particles incorporated is non-trivial. Finally, we illustrate how these results can provide insights into studying a network with multiple pools.

Characterization of Alternaria blotch disease of apple in Himachal Pradesh, India: insights on morphology, pathogenicity, and molecular features.

BACKGROUND: Alternaria blotch disease in Himachal Pradesh, India, caused by Alternaria spp., adversely affects apple cultivars, resulting in reduced fruit size and quality accompanied by premature leaf fall. METHODS AND RESULTS: Sixteen Alternaria isolates from apple growing regions underwent comprehensive analysis including morphology, pathogenicity, and molecular characterization. Variations in conidiophore and conidia dimensions, shapes, and divisions were observed among isolates. Pathogenicity assays revealed differences in incubation periods, latent phases, and disease responses. Molecular characterization via nuclear ITS rDNA and RAPD analysis indicated 99-100% homology with Alternaria alternata, Alternaria mali, and other Alternaria spp., with a close phylogenetic relationship to Chinese isolates. Differentiation of isolates based on origin, cultural characteristics, and morphology was achieved using RAPD markers. CONCLUSIONS: The study identifies diverse genotypes and morphotypes of Alternaria contributing to apple blotch disease in Himachal Pradesh. These findings highlight the complexity of the pathogenic environment and hold significant implications for disease management in apple orchards.

Competition for resources in an exclusion model with biased lane-changing mechanism.

The motivation for the proposed work is drawn from the attachment-detachment observed in biological and physical transport processes that entail finite resources. We investigate the influence of limited particle availability on particle dynamics within two parallel totally asymmetric simple exclusion lanes, with one lane incorporating only particle detachment and the other considering particle attachment. We establish a theoretical framework by employing vertical mean-field theory in conjunction with singular perturbation technique. The analytical findings are supported by numerical and stochastic validation using a finite-difference scheme and the Gillespie algorithm. By utilizing these approaches, we scrutinize various stationary properties, including particle densities, phase boundaries, and particle currents for both lanes. Our analysis reveals that the complexity of the phase diagram exhibits a nonmonotonic trend in the number of stationary phases as the particle count increases. Each phase diagram is constructed with respect to the intrinsic boundary parameters, illustrating both bulk and surface transitions occurring within the lanes. The interplay between finite resources and coupling mechanisms gives rise to two phases involving upward shock in one of the lanes, while two phases exhibit synchronized downward shock in both lanes. Finally, we delve into shock dynamics to comprehend critical phase transitions occurring in the system.

Totally asymmetric simple exclusion process with local resetting in a resource-constrained environment.

Inspired by the process of mRNA translation, in which the stochastic degradation of mRNA-ribosome machinery is modeled by the resetting dynamics, we study an open totally asymmetric simple exclusion process with local resetting at the entry site in a resource-constrained environment. The effect of constrained resources on the stationary properties of the system has been comprehended in the form of the filling factor. The mean-field approximations are utilized to obtain stationary state features, such as density profiles and phase diagrams. The phase diagram possesses pure phases as well as coexisting phases, including a low-density-high-density phase separation, which did not manifest under periodic boundary conditions despite the system being closed there as well. The role of the resetting rate has been investigated on the stationary properties of the system, depending on how the filling factor scales with the system size. In contrast to the resetting model for infinite resources, two distinct phase transitions are observed for the smaller values of the filling factor leading to a change in the topology of the phase diagram. The impact of the resetting rate along with the finite-size effect has also been examined on the shock dynamics. All the mean-field results are found in remarkable agreement with the Monte Carlo simulations.

Tailoring the Photophysical Properties of a Homoleptic Iron(II) Tetra N-Heterocyclic Carbene Complex by Attaching an Imidazolium Group to the (C∧N∧C) Pincer Ligand─A Comparative Study.

We here report the synthesis of the homoleptic iron(II) N-heterocyclic carbene (NHC) complex [Fe(miHpbmi)2](PF6)4 (miHpbmi = 4-((3-methyl-1H-imidazolium-1-yl)pyridine-2,6-diyl)bis(3-methylimidazol-2-ylidene)) and its electrochemical and photophysical properties. The introduction of the π-electron-withdrawing 3-methyl-1H-imidazol-3-ium-1-yl group into the NHC ligand framework resulted in stabilization of the metal-to-ligand charge transfer (MLCT) state and destabilization of the metal-centered (MC) states. This resulted in an improved excited-state lifetime of 16 ps compared to the 9 ps for the unsubstituted parent compound [Fe(pbmi)2](PF6)2 (pbmi = (pyridine-2,6-diyl)bis(3-methylimidazol-2-ylidene)) as well as a stronger MLCT absorption band extending more toward the red spectral region. However, compared to the carboxylic acid derivative [Fe(cpbmi)2](PF6)2 (cpbmi = 1,1'-(4-carboxypyridine-2,6-diyl)bis(3-methylimidazol-2-ylidene)), the excited-state lifetime of [Fe(miHpbmi)2](PF6)4 is the same, but both the extinction and the red shift are more pronounced for the former. Hence, this makes [Fe(miHpbmi)2](PF6)4 a promising pH-insensitive analogue of [Fe(cpbmi)2](PF6)2. Finally, the excited-state dynamics of the title compound [Fe(miHpbmi)2](PF6)4 was investigated in solvents with different viscosities, however, showing very little dependency of the depopulation of the excited states on the properties of the solvent used.

How Rigidity and Conjugation of Bidentate Ligands Affect the Geometry and Photophysics of Iron N-Heterocyclic Complexes: A Comparative Study.

Two iron complexes featuring the bidentate, nonconjugated N-heterocyclic carbene (NHC) 1,1'-methylenebis(3-methylimidazol-2-ylidene) (mbmi) ligand, where the two NHC moieties are separated by a methylene bridge, have been synthesized to exploit the combined influence of geometric and electronic effects on the ground- and excited-state properties of homoleptic FeIII-hexa-NHC [Fe(mbmi)3](PF6)3 and heteroleptic FeII-tetra-NHC [Fe(mbmi)2(bpy)](PF6)2 (bpy = 2,2'-bipyridine) complexes. They are compared to the reported FeIII-hexa-NHC [Fe(btz)3](PF6)3 and FeII-tetra-NHC [Fe(btz)2(bpy)](PF6)2 complexes containing the conjugated, bidentate mesoionic NHC ligand 3,3'-dimethyl-1,1'-bis(p-tolyl)-4,4'-bis(1,2,3-triazol-5-ylidene) (btz). The observed geometries of [Fe(mbmi)3](PF6)3 and [Fe(mbmi)2(bpy)](PF6)2 are evaluated through L-Fe-L bond angles and ligand planarity and compared to those of [Fe(btz)3](PF6)3 and [Fe(btz)2(bpy)](PF6)2. The FeII/FeIII redox couples of [Fe(mbmi)3](PF6)3 (-0.38 V) and [Fe(mbmi)2(bpy)](PF6)2 (-0.057 V, both vs Fc+/0) are less reducing than [Fe(btz)3](PF6)3 and [Fe(btz)2(bpy)](PF6)2. The two complexes show intense absorption bands in the visible region: [Fe(mbmi)3](PF6)3 at 502 nm (ligand-to-metal charge transfer, 2LMCT) and [Fe(mbmi)2(bpy)](PF6)2 at 410 and 616 nm (metal-to-ligand charge transfer, 3MLCT). Lifetimes of 57.3 ps (2LMCT) for [Fe(mbmi)3](PF6)3 and 7.6 ps (3MLCT) for [Fe(mbmi)2(bpy)](PF6)2 were probed and are somewhat shorter than those for [Fe(btz)3](PF6)3 and [Fe(btz)2(bpy)](PF6)2. [Fe(mbmi)3](PF6)3 exhibits photoluminescence at 686 nm (2LMCT) in acetonitrile at room temperature with a quantum yield of (1.2 ± 0.1) × 10-4, compared to (3 ± 0.5) × 10-4 for [Fe(btz)3](PF6)3.

Ferrous and ferric complexes with cyclometalating N-heterocyclic carbene ligands: a case of dual emission revisited.

Iron N-heterocyclic carbene (FeNHC) complexes with long-lived charge transfer states are emerging as a promising class of photoactive materials. We have synthesized [FeII(ImP)2] (ImP = bis(2,6-bis(3-methylimidazol-2-ylidene-1-yl)phenylene)) that combines carbene ligands with cyclometalation for additionally improved ligand field strength. The 9 ps lifetime of its 3MLCT (metal-to-ligand charge transfer) state however reveals no benefit from cyclometalation compared to Fe(ii) complexes with NHC/pyridine or pure NHC ligand sets. In acetonitrile solution, the Fe(ii) complex forms a photoproduct that features emission characteristics (450 nm, 5.1 ns) that were previously attributed to a higher (2MLCT) state of its Fe(iii) analogue [FeIII(ImP)2]+, which led to a claim of dual (MLCT and LMCT) emission. Revisiting the photophysics of [FeIII(ImP)2]+, we confirmed however that higher (2MLCT) states of [FeIII(ImP)2]+ are short-lived (<10 ps) and therefore, in contrast to the previous interpretation, cannot give rise to emission on the nanosecond timescale. Accordingly, pristine [FeIII(ImP)2]+ prepared by us only shows red emission from its lower 2LMCT state (740 nm, 240 ps). The long-lived, higher energy emission previously reported for [FeIII(ImP)2]+ is instead attributed to an impurity, most probably a photoproduct of the Fe(ii) precursor. The previously reported emission quenching on the nanosecond time scale hence does not support any excited state reactivity of [FeIII(ImP)2]+ itself.

Allosteric Determinants in High Temperature Requirement A Enzymes Are Conserved and Regulate the Population of Active Conformations.

High temperature requirement A (HtrA) are allosterically regulated enzymes wherein effector binding to the PDZ domain triggers proteolytic activity. Yet, it remains unclear if the inter-residue network governing allostery is conserved across HtrA enzymes. Here, we investigated and identified the inter-residue interaction networks by molecular dynamics simulations on representative HtrA proteases, Escherichia coli DegS and Mycobacterium tuberculosis PepD, in effector-bound and free forms. This information was used to engineer mutations that could potentially perturb allostery and conformational sampling in a different homologue, M. tuberculosis HtrA. Mutations in HtrA perturbed allosteric regulation─a finding consistent with the hypothesis that the inter-residue interaction network is conserved across HtrA enzymes. Electron density from data collected on cryo-protected HtrA crystals revealed that mutations altered the topology of the active site. Ensemble models fitted into electron density calculated from room-temperature diffraction data showed that only a fraction of these models had a catalytically competent active site conformation alongside a functional oxyanion hole thus providing experimental evidence that these mutations influenced conformational sampling. Mutations at analogous positions in the catalytic domain of DegS perturbed the coupling between effector binding and proteolytic activity, thus confirming the role of these residues in the allosteric response. The finding that a perturbation in the conserved inter-residue network alters conformational sampling and the allosteric response suggests that an ensemble allosteric model best describes regulated proteolysis in HtrA enzymes.

Association between neutrophil lymphocyte ratio and status of symptom control in children and adolescents with bronchial asthma.

Neutrophil lymphocyte ratio (NLR), an easy and readily available biomarker of systemic inflammation, has been less studied so far as a putative marker of asthma control. Our study aimed to assess its feasibility. A total of 90 asthmatic children, aged 5-18 years, diagnosed according to Global Initiative for Asthma (GINA) guidelines, were. Control status of asthma was assessed using the asthma control test (ACT) or childhood ACT and categorized as controlled group-1 (ACT > 19) and uncontrolled group-2 (ACT ≤ 19). The difference between mean values in both groups was analysed, finding a significant difference between children with and without a family history (p = 0.004) and those with and without a need for admission (p = 0.045). Also, a significant association was established between NLR and the type of severity of asthma (p = 0.049), but none between NLR and age, gender, BMI, coexisting allergic rhinitis, or asthma exacerbation. Thus we found no significant association between NLR and symptom control status. However, NLR has the potential to be a putative marker of inflammation, although its relative status to CRP needs further studies.

Interplay of reservoirs in a bidirectional system.

Motivated by the interplay of multiple species in several real world transport processes, we propose a bidirectional totally asymmetric simple exclusion process with two finite particle reservoirs regulating the inflow of oppositely directed particles corresponding to two different species. The system's stationary characteristics, such as densities, currents, etc., are investigated using a theoretical framework based on mean-field approximation and are supported by extensive Monte Carlo simulations. The impact of individual species populations, quantified by filling factor, has been comprehensively analyzed considering both equal and unequal conditions. For the equal case, the system exhibits the spontaneous symmetry-breaking phenomena and admits both symmetric as well as asymmetric phases. Moreover, the phase diagram exhibits a different asymmetric phase and displays a nonmonotonic variation in the number of phases with respect to the filling factor. For unequal filling factors, the phase schema can display at most five phases including a phase that shows maximal current for one of the species.

Modeling mRNA Translation With Ribosome Abortions.

We derive a deterministic mathematical model for the flow of ribosomes along a mRNA called the ribosome flow model with extended objects and abortions (RFMEOA). This model incorporates important cellular features such as every ribosome covers several codons and they may detach from various regions along the track due to more realistic biological situations including phenomena of ribosome-ribosome collisions. We prove that the ribosome density profile along the mRNA in the RFMEOA and in particular, the protein production rate converge to a unique steady-state. Simulations of the RFMEOA demonstrate a surprising result that an increase in the initiation rate may sometimes lead to a decrease in the production rate. We believe that this model could be helpful to provide insight into the effects of premature termination on the protein expression and be useful for understanding and re-engineering the translation process.

Modelling of transport processes: Theory and simulations.

The transport processes, being a non-equilibrium system, have been a point of interest for physicists since many years revealing and explaining several unexpected effects. Such systems are often dealt with an archetypal model, known as totally asymmetric simple exclusion process, with two different types of boundary conditions: open and periodic. Moreover, these models are analyzed in two varieties of dynamics, random sequential and parallel updates, even at the micro level which play an important role in the global dynamics of the system. On contrary to the random sequential rule, the parallel updates introduce correlations in the system. Using theoretical and numerical methods in the framework based on mean-field approaches, the system properties are analyzed in both transient and steady state.•Both the updating rules are realized using Monte Carlo simulations.•In simplest form, mean-field approach ignores all the correlations and the results coincide with the random sequential update.•Correlations are induced in the system due to parallel update, therefore, a cluster mean-field theory is also discussed to handle them.

Exclusion processes on a roundabout traffic model with constrained resources.

Motivated by the vehicular traffic phenomenon at roundabouts, we examine how the limited availability of resources affects the movement of two distinct types of particles on bidirectional lanes connected by two bridges, with each bridge specifically designated for the transportation of one species. To provide a theoretical ground for our findings, we employ a mean-field framework and successfully validate them through dynamic Monte Carlo simulations. Based on the theoretical analysis, we analytically derive various stationary properties, such as the particle densities, phase boundaries, and particle currents, for all the possible symmetric as well as asymmetric phases. The qualitative as well as quantitative behavior of the system is significantly affected by the constraint on the number of resources. The complexity of the phase diagram shows a nonmonotonic behavior with an increasing number of particles in the system. Analytical arguments enable the identification of several critical values for the total number of particles, leading to a qualitative change in the phase diagrams. The interplay of the finite resources and the bidirectional transport yields unanticipated and unusual features such as back-and-forth transition, the presence of two congested phases where particle movement is halted, as well as shock phases induced by boundaries and the bulk of the system. Also, it is found that spontaneous symmetry-breaking phenomena are induced even for very few particles in the system. Moreover, we thoroughly examine the location of shocks by varying the parameters controlling the system's boundaries, providing insights into possible phase transitions.

Flow Cytometric Expression of CD49d in Newly Diagnosed Chronic Lymphocytic Leukemia and Its Correlation with Established Prognostic Markers.

Introduction Chronic lymphocytic leukemia (CLL) is the commonest hematological malignancy in the West but is relatively uncommon in India. The prognosis of CLL is determined by well-established prognostic markers. CD49d has been emerging as a promising prognostic marker in CLL. CD49d expression in CLL has been found to have an aggressive clinical course, shorter time to first treatment, and poorer prognosis. The aim of this study was to analyze the flow cytometric expression of CD49d in newly diagnosed CLL and to correlate its expression with clinico-hematological parameters. Materials and Methods Twenty-five consecutive patients of CLL, diagnosed on flow cytometry, were included in the study. Patients on treatment or those with relapse were excluded. The panel for flow cytometry included the routine markers used for CLL diagnosis along with CD49d. The expression of CD49d was correlated with clinico-hematological parameters in all patients. "R" software was used for the statistical analysis. Fisher's exact test and Wilcox test were used to assess the correlation of CD49d to categorical and continuous data, respectively. Results The mean age of the patients was 62.6 ± 12.5 years, and 80% were symptomatic at diagnosis. CD49d expression was found in 44% cases, with a higher proportion being male patients. CD49d and prolymphocyte percentage showed a statistically significant correlation ( p = 0.0007). We found a statistically significant correlation between CD49d expression and lymphadenopathy and splenomegaly with p -values of 0.033 and 0.0472, respectively. CD49d positivity correlated significantly with a higher Rai stage ( p = 0.0196) and intermediate and high-risk cases according to Binet staging ( p = 0.033). Conclusion CD49d expression in the present study correlated with a higher prolymphocyte percentage, lymphadenopathy, splenomegaly, and higher Rai and Binet stages. CD49d expression on flow cytometry was reproducible and easy to interpret.

Reservoir crowding in a resource-constrained exclusion process with a dynamic defect.

To understand the complicated transport processes that occur in biological and physical systems, we investigate a constrained totally asymmetric simple exclusion process with a stochastic defect particle. The defect particle might randomly emerge or vanish, resulting in a dynamic defect, and slows down the flow of moving particles when attached to the lattice. Using a mean-field technique, we examine the steady-state characteristics and boundary-layer analysis is provided to comprehend the properties of finite system. In a simplification, our theoretical method unifies three different parameter used to define the defect dynamics into one parameter termed the obstruction factor. It is found that the defect kinetics lead to emergence of phases where the current is defect restricted. The system shows nine phases overall, including bulk-induced and boundary-induced shock phases, with the phase schema showing no more than eight phases depending on the dynamics. We found that variation of obstruction does not lead to qualitative transition in the system, whereas the change in constraint on total particles affect the system qualitatively. All the theoretical outcomes have been validated using extensive Monte Carlo simulations.

Photophysical Integrity of the Iron(III) Scorpionate Framework in Iron(III)-NHC Complexes with Long-Lived 2LMCT Excited States.

Fe(III) complexes with N-heterocyclic carbene (NHC) ligands belong to the rare examples of Earth-abundant transition metal complexes with long-lived luminescent charge-transfer excited states that enable applications as photosensitizers for charge separation reactions. We report three new hexa-NHC complexes of this class: [Fe(brphtmeimb)2]PF6 (brphtmeimb = [(4-bromophenyl)tris(3-methylimidazol-2-ylidene)borate]-, [Fe(meophtmeimb)2]PF6 (meophtmeimb = [(4-methoxyphenyl)tris(3-methylimidazol-2-ylidene)borate]-, and [Fe(coohphtmeimb)2]PF6 (coohphtmeimb = [(4-carboxyphenyl)tris(3-methylimidazol-2-ylidene)borate]-. These were derived from the parent complex [Fe(phtmeimb)2]PF6 (phtmeimb = [phenyltris(3-methylimidazol-2-ylidene)borate]- by modification with electron-withdrawing and electron-donating substituents, respectively, at the 4-phenyl position of the ligand framework. All three Fe(III) hexa-NHC complexes were characterized by NMR spectroscopy, high-resolution mass spectroscopy, elemental analysis, single crystal X-ray diffraction analysis, electrochemistry, Mößbauer spectroscopy, electronic spectroscopy, magnetic susceptibility measurements, and quantum chemical calculations. Their ligand-to-metal charge-transfer (2LMCT) excited states feature nanosecond lifetimes (1.6-1.7 ns) and sizable emission quantum yields (1.7-1.9%) through spin-allowed transition to the doublet ground state (2GS), completely in line with the parent complex [Fe(phtmeimb)2]PF6 (2.0 ns and 2.1%). The integrity of the favorable excited state characteristics upon substitution of the ligand framework demonstrates the robustness of the scorpionate motif that tolerates modifications in the 4-phenyl position for applications such as the attachment in molecular or hybrid assemblies.