Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study

Uranium is routinely handled in various stages of nuclear fuel cycle and its association with human serum albumin (HSA) has been reported in literature, however, their binding characteristics still remains obscure. The present study aims to understand interaction of uranium with HSA by employing all atom molecular dynamics simulation of the HSA-metal ion complex. His67, His247 and Asp249 residues constitute the major binding site of HSA, which capture the uranyl ion (UO22+). A total of six sets of initial coordinates are used for Zn2+-HSA and UO22+-HSA system at pH = 4, 7.4 and 9, respectively. Enhance sampling method, namely, well-tempered meta-dynamics (WT-MtD) is employed to study the binding and un-binding processes of UO22+ and Zn2+ ions. Potential of mean force (PMF) profiles are generated for all the six sets of complexes from the converged WT-MtD run. Various basins and barriers are observed along the (un)binding pathways. Hydrogen bond dynamics and short-range Coulomb interactions are evaluated from the equilibrium run at each basins and barriers for both the ions at all pH values. The binding of UO22+ ion with HSA is the result of the dynamical balance between UO22+-HSA and UO22+-water short range Coulomb interactions. Zn2+ ion interact more strongly than UO22+ at all pH through short range Coulomb interactions. PMF values further concludes that UO22+ cannot associate to the Zn2+ bound HSA protein but can be captured by free HSA at all pH values i.e. endosomal, alkaline and physiological pH.Communicated by Ramaswamy H. Sarma.

Heat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation

The capsid-like structure of the virus-based protein nanoparticles (NPs) can serve as bionanomaterials, with applications in biomedicines and nanotechnology. Release of packaged material from these nanocontainers is associated with subtle conformational changes of the NP structure, which in vitro, is readily accomplished by heating. Characterizing the structural changes as a function of temperature may provide fresh insights into nanomaterial/antiviral strategies. Here, we have calculated heat induced changes in the properties of an empty minute virus of mice particle using large-scale ≈ 3.0 × 10⁶ all-atom molecular dynamics simulations. We focus on two heat induced structural changes of the NP, namely, dynamical transition (DT) and breathing transition (BT), both characterized by sudden and sharp change of measured parameters at temperatures, T_DT and T_BT, respectively. While DT is assessed by mean-square fluctuation of hydrogen atoms of the NP, BT is monitored through internal volume and permeation rate of water molecules through the NP. Both the transitions, resulting primarily from collective atomistic motion, are found to occur at temperatures widely separated from one another (T_BT>T_DT). The breathing motions, responsible for the translocation events of the packaged materials through the NP to kick off, are further probed by computing atomic resolution stresses from NVE simulations. Distribution of equilibrium atomistic stresses on the NP reveals a largely asymmetric nature and suggests structural breathing may actually represent large dynamic changes in the hotspot regions, far from the NP pores, which is in remarkable resemblance with recently conducted hydrogen-deuterium exchange coupled to mass spectrometry experiment. Communicated by Ramaswamy H. Sarma.

Adjuvant therapy in neonatal sepsis to prevent mortality - A systematic review and network meta-analysis

BACKGROUND

Despite appropriate antibiotic therapy, the risk of mortality in neonatal sepsis still remains high. We conducted a systematic review to comprehensively evaluate different adjuvant therapies in neonatal sepsis in a network meta-analysis.

METHODS

We included randomized controlled trials (RCTs) and quasi-RCTs that evaluated adjuvant therapies in neonatal sepsis. Neonates of all gestational and postnatal ages, who were diagnosed with sepsis based on blood culture or sepsis screen were included. We searched MEDLINE, CENTRAL, EMBASE and CINAHL until 12th April 2021 and reference lists. Data extraction and risk of bias assessment were performed in duplicate. A network meta-analysis with bayesian random-effects model was used for data synthesis. Certainty of evidence (CoE) was assessed using GRADE.

RESULTS

We included 45 studies involving 6,566 neonates. Moderate CoE showed IVIG [Relative Risk (RR); 95% Credible Interval (CrI): 1.00; (0.67-1.53)] as an adjunctive therapy probably does not reduce all-cause mortality before discharge, compared to standard care. Melatonin [0.12 (0-0.08)] and granulocyte transfusion [0.39 (0.19-0.76)] may reduce mortality before discharge, but CoE is very low. The evidence is also very uncertain regarding other adjunctive therapies to reduce mortality before discharge. Pentoxifylline may decrease the duration of hospital stay [Mean difference; 95% CrI: -7.48 days (-14.50-0.37)], but CoE is very low.

CONCLUSION

Given the biological plausibility for possible efficacy of these adjuvant therapies and that the CoE from the available trials is very low to low except for IVIG, we need large adequately powered RCTs to evaluate these therapies in sepsis in neonates.

Unbinding of hACE2 and inhibitors from the receptor binding domain of SARS-CoV-2 spike protein

The first direful biomolecular event leading to COVID-19 disease is the SARS-CoV-2 virus surface spike (S) protein-mediated interaction with the human transmembrane protein, angiotensin-converting enzyme 2 (hACE2). Prevention of this interaction presents an attractive alternative to thwart SARS-CoV-2 replications. The development of monoclonal antibodies (mAbs) in the convalescent plasma treatment, nanobody, and designer peptides, which recognizes epitopes that overlap with hACE2 binding sites in the receptor-binding domain (RBD) of S protein (S/RBD) and thereby blocking the infection has been the center stage of therapeutic research. Here we report atomistic and reliable in silico structure-energetic features of the S/RBD interactions with hACE2 and its two inhibitors (convalescent mAb, B38, and an alpaca nanobody, Ty1). The discovered potential of mean forces exhibits free energy basin and barriers along the interaction pathways, providing sufficient molecular insights to design a B38 mutant and a Ty1-based peptide with higher binding capacity. While the mutated B38 forms a 60-fold deeper free energy minimum, the designer peptide (Ty1-based) constitutes 38 amino acids and is found to form a 100-fold deeper free energy minimum in the first binding basin than their wild-type variants in complex with S/RBD. Our strategy may help to design more efficacious biologics towards therapeutic intervention against the current raging pandemic.Communicated by Ramaswamy H. Sarma.

MD simulation reveals differential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH

The iron carrier human serum transferrin (sTf) is known to transport other metals, including some actinides (An). Radiotoxic An are routinely involved in the nuclear fuel cycle and the possibility of their accidental exposure cannot be ruled out. Understanding An interaction with sTf assumes a greater significance for the development of safe and efficacious chelators for their removal from the blood stream. Here we report several 100 ns equilibrium MD simulations of Cm(III)- and Th(IV)-loaded sTf at various protonation states of the protein to explore the possibility of the two An ions release and speciation. The results demonstrate variation in protonation state of dilysine pair (K206 and K296) and the tyrosine (Y188) residue is necessary for the opening of Cm(III)-bound protein and the release of the ion. For the tetravalent thorium, protonation of dilysine pair suffices to cause conformational changes of protein. However, in none of the protonation states, Th(IV) releases from sTf because of its strong electrostatic interaction with D63 in the first shell of the sTf binding cleft. Analysis of hydrogen bond, water bridge, and the evaluation of potential of mean forces of the An ions' release from sTf, substantiate the differential behavior of Cm(III) and Th(IV) at endosomal pH. The results provide insight in the regulation of Cm(III) and Th(IV) bioavailability that may prove useful for effective design of their decorporating agents and as well may help the future design of radiotherapy based on tetravalent ions.

Molecular dynamics simulations of plutonium binding and its decorporation from the binding-cleft of human serum transferrin

The possibility of plutonium (Pu) intake by radiation workers can not be ruled out. Transportation of Pu(IV) to various organs/cells is mainly carried through iron-carrying protein, serum transferrin (sTf), by receptor-mediated endocytosis. Understanding the Pu-sTf interaction is a primary step toward future design of its decorporating agents. We report MD simulations of Pu(IV) binding with sTf and look out for its decorporation at extracellular pH using suitable ligands. MD simulations were carried out in polarizable water environment at different protonation states of the protein. Results unravel the binding motif of Pu(IV): (1) sTf binds the ion in closed conformation at extracellular serum pH with carbonate as synergistic anions, (2) change in protonation state of dilysine (K206 and K296)-trigger and that of the carbonate ion at acidic endosomal pH is found to cause conformational changes of protein, conducive for the heavy ion to be released, although; (3) strong electrostatic interaction between D63 in the binding-cleft and Pu(IV) is found not to ever set free the ion. In an endeavour to decorporate Pu(IV), fragmented molecular form of hydroxypyridinone (HOPO) and catechol (CAM)-based ligands are docked at the binding site (BS) of the protein and metadynamics simulations are conducted. Pu(IV) binding at BS is found to be so strong that it was not detached from BS with the docked HOPO. However, for the identical set of simulation parameters, CAM is found to facilitate dislodging the heavy ion from the protein's binding influence. Differential behaviour of the two chelators is further explored. Fragmented molecular form of hydroxy-pyridinone (HOPO) and catecholamide (CAM) ligands were docked at the binding-site (BS) of human serum transferrin (sTf) to explore their feasibility as plausible Pu(IV) decorporating agents by employing metadynamics method. CAM was found to dislodge Pu from the sTf BS, while HOPO could not.

Correlation of functional echocardiography and clinical parameters in term neonates with shock

BACKGROUND

To evaluate the correlation between functional echocardiography and clinical parameters in term neonates with shock.

METHOD

Cross sectional study of 30 full term newborns who were clinically detected to have shock compared to 30 full term hemodynamically stable neonates. For statistical analysis, cases were further sub classified into cardiogenic and septic shock.

RESULT

Functional echocardiography revealed inferior vena cava collapsibility index (cIVC), fractional shortening (FS), ejection fraction (EF), cardiac output and superior vena cava (SVC) flow were significantly lower whereas myocardial performance index (MPI) was significantly higher in babies with cardiogenic and septic shock as compared to the controls. Left ventricular end diastolic area (LVEDA) was significantly higher in cardiogenic shock whereas it was significantly lower in septic shock as compared to the controls. Also, cIVC was significantly lower and LVEDA was significantly higher in cardiogenic as compared to the septic shock. In cardiogenic shock SVC flow correlated significantly with capillary filling time and systolic blood pressure. The correlation between functional echocardiographic parameters of cardiogenic and septic shock showed that EF, FS and MPI were positively and significantly correlated (r 0.742, p 0.022 for EF, r 0.766, p 0.016 for FS and r 0.478, p 0.05 for MPI) whereas SVC flow and cIVC were negatively and significantly correlated between cardiogenic and septic shock (r - 0.655, p 0.045 for SVC flow and - 0.578, p 0.05 for cIVC).

CONCLUSION

In the complex environment of neonatal intensive care unit detection of shock continues to be a major challenge. Functional echocardiography provides an adjunct information to the clinical assessment of shock and helps in monitoring the response to treatment.

Quantum chemical and well-tempered metadynamics study to design adenine analogs for orthogonal Preq1 riboswitch

Communicated by Ramaswamy H. Sarma.

Binding of Cm(III) and Th(IV) with Human Transferrin at Serum pH: Combined QM and MD Investigations

Human serum transferrin (sTf) can also function as a noniron metal transporter since only 30% of it is typically saturated with a ferric ion. While this function of sTf can be fruitfully utilized for targeted delivery of certain metal therapeutics, it also runs the risk of trafficking the lethal radionuclides into cells. A large number of actinide (An) ions are known to bind to the iron sites of sTf although molecular-level understanding of their binding is unclear. Understanding the radionuclide interaction with sTf is a primary step toward future design of their decorporating agents since irrespective of the means of contamination, the radionuclides are absorbed and transported by blood before depositing into target organs. Here, we report an extensive multiscale modeling approach of two An (curium(III) and thorium(IV)) ions' binding with sTf at serum physiological pH. We find that sTf binds both the heavy ions in a closed conformation with carbonate as synergistic anions and the An-loaded sTf maintains its closed conformation even after 100 ns of equilibrium molecular dynamics (MD) simulations. MD simulations are performed in a polarizable water environment, which also incorporates electronic continuum corrections for ions via charge rescaling. The molecular details of the An coordination and An exchange free energies with iron in the interdomain cleft of the protein are evaluated through a combination of quantum mechanical (QM) and MD studies. In line with reported experimental observations, well-tempered metadynamics results of the ions' binding energetics show that An-sTf complexes are less stable than Fe-sTf. Additionally, curium(III) is found to bind more weakly than thorium(IV). The latter result might suggest relative attenuation of thorium(IV) cytotoxicity when compared with curium(III).

Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water

Temperature induced dynamical transition (DT), associated with a sharp rise in molecular flexibility, is well-known to be exhibited between 270 and 280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies is described by empirical nonpolarizable force fields in which electronic polarizability is treated implicitly with effective charges and related parameters. This might have led to the present trait of discovery that DTs of biomolecules, irrespective of the potential functions for water models used, occur within a narrow band of temperature variation (30-40 K). Whereas a water molecule in a biomolecular surface and one in bulk are polarized differently, therefore explicit treatment of water polarizability would be a powerful approach toward the treatment of hydration water, believed to cause the DT manifestation. Using MD simulations, we investigated the effects of polarizable water on the DT of biomolecules and the dynamic properties of hydration water. We chose two types of solutes: globular protein (lysozyme) and more open and flexible RNAs (a hairpin and a riboswitch) with different natures of hydrophilic sites than proteins in general. We found that the characteristic temperature of DT ( T_DT) for the solutes in polarizable water is always higher than that in its nonpolarizable counterpart. In particular, for RNAs, the variations are found to be ∼45 K between the two water models, whereas for the more compact lysozyme, it is only ∼4 K. The results are discussed in light of the enormous increase in relaxation times of a liquid upon cooling in the paradigm of dynamic switchover in hydration water with liquid-liquid phase transition, derived from the existence of the second critical point. Our result supports the idea that structures of biomolecules and their interactions with the hydration water determines T_DT and provides evidence for the decisive role of polarizable water on the onset of DT, which has been hitherto ignored.

Distribution, antimicrobial resistance and predictors of mortality in neonatal sepsis

OBJECTIVE

The aim of this study is to investigate etiological agents, patterns of antimicrobial resistance and predictors of mortality in culture proven neonatal sepsis.

METHOD

This is a twenty-four month retrospective cohort study of infants with culture proven sepsis. Demographic data, type of isolates and its sensitivity pattern were recorded. Multidrug resistant gram-negative isolates were defined as resistance to any three of five antibiotic classes: extended-spectrum cephalosporins, carbapenems, aminoglycosides, fluoroquinolones and piperacillin-tazobactam.

RESULT

A total of 183 case with culture positive sepsis were identified. Early onset sepsis occurred in 59% of cases. The majority of isolates (56.2%) were gram-positive but the most common individual isolates were klebsiella spp. (31.1%), Staphylococcus aureus (24.5%) and coagulase-negative staphylococci (CONS) (22.9%). The pathogen mix in early-onset did not differ from late-onset sepsis. High rates of multidrug resistance were observed in klebsiella spp. (49.1%), Escherichia coli (50%), citrobacter spp (50%), acinetobacter spp. (28.5%), pseudomonas spp. (100%) isolates. Methicillin resistance prevailed in 16.6% of coagulase-negative staphylococci, 24.4% of Staphylococcus aureus and 62.5% of enterococcus spp. Multivariate analysis revealed invasive ventilation and early onset sepsis to be independently associated with increased risk of mortality in contrast to breast milk feeding which is associated with decreased risk of mortality.

CONCLUSION

A high degree of antimicrobial resistance underscores the need to understand the pathogenesis of resistance, curtail the irrational prescription of antibiotics in neonates and the requirement for measures to prevent it in low-income and middle-income countries.

Stereoselective Metabolism of Omeprazole by Cytochrome P450 2C19 and 3A4: Mechanistic Insights from DFT Study

The efficacy of S-omeprazole as a proton pump inhibitor compared with that of its enantiomer R-omeprazole is studied using density functional theoretical calculations. The pharmacokinetic studies suggest that the efficacy of S-omeprazole presumably depends on metabolic pathway and excretion from the human body. The density functional theory calculations at SMD_water-B3LYP-D3/6-311+G(d,p)/LANL2DZ//B3LYP/6-31G(d)/LANL2DZ with triradicaloid model active species, [Por^•+Fe^IV(SH)O], of CYP2C19 enzyme with high-spin quartet and low-spin doublet states demonstrate C-H bond activation mechanism through a two-state rebound process for the hydroxylation of R-omeprazole and S-omeprazole. The calculated activation free energy barriers for the hydrogen abstraction are 15.7 and 17.5 kcal/mol for R-omeprazole and S-omeprazole, respectively. The hydroxylation of R-omeprazole and S-omeprazole is thermodynamically favored; however, the hydroxylated intermediate of S-omeprazole further disintegrates to metabolite 5- O-desmethylomeprazole with a higher kinetic barrier. We have examined the sulfoxidation of S-omeprazole to omeprazole sulfone metabolite by CYP3A4, and the observed activation free energy barrier is 9.9 kcal/mol. The computational results reveal that CYP2C19 exclusively metabolizes R-omeprazole to hydroxyomeprazole, which is hydrophilic and can easily excrete, whereas CYP3A4 metabolizes S-omeprazole to lipophilic sulfone; hence, the excretion of this metabolite would be relatively slower from the body. The spin density analysis and molecular orbital analysis performed using biorthogonalization calculations indicate that R-omeprazole favors high-spin pathway for metabolism process whereas S-omeprazole prefers the low-spin pathway.

Designed inhibitors with hetero linkers for gastric proton pump H+,K+-ATPase: Steered molecular dynamics and metadynamics studies

Acid suppressant SCH28080 and its derivatives reversibly reduce acid secretion activity of the H⁺,K⁺-ATPase in a K⁺ competitive manner. The results on homologation of the SCH28080 by varying the linker chain length suggested the improvement in efficacy. However, the pharmacokinetic studies reveal that the hydrophobic nature of the CH₂ linker units may not help it to function as a better acid suppressant. We have exploited the role of linker unit to enhance the efficacy of such reversible acid suppressant drug molecules using hetero linker, i.e., disulfide and peroxy linkers. The logarithm of partition coefficient defined for a drug molecule relates to the partition coefficient, which allows the optimum solubility characteristics to reach the active site. The logarithm of partition coefficient calculated for the designed inhibitors suggests that inhibitors would possibly reach the active site in sufficient concentration like in the case of SCH28080. The steered molecular dynamics studies have revealed that the Inhibitor-1 with disulfide linker unit is more stable at the active site due to greater noncovalent interactions compared to the SCH28080. Centre of mass distance analysis suggests that the Cysteine-813 amino acid residue selectively plays an important role in the inhibition of H⁺,K⁺-ATPase for Inhibitor-1. Furthermore, the quantum chemical calculations with M11L/6-31+G(d,p) level of theory have been performed to account the noncovalent interactions responsible for the stabilization of inhibitor molecules in the active site gorge of the gastric proton pump at different time scale. The hydrogen bonding and hydrophobic interaction studies corroborate the center of mass distance analysis as well. Well-tempered metadynamics free energy surface and center of mass separation analysis for the Inhibitor-1 is in good agreement with the steered molecular dynamics results. The torsional angle of the linker units seems to be crucial for better efficacy of drug molecules. The torsional angle of linker units of SCH28080 (COCH₂C) and of Inhibitor 1 (CSSC) prefers to lie within ∼60°-90° for a longer time during the simulations, whereas, the peroxy linker (COOC) of Inhibitor 2 prefers to adopt ∼120-160°. Therefore, it appears that the smaller torsion angle of linker units can achieve better interactions with the active site residues of H⁺,K⁺-ATPase to inhibit the acid secretion activity. The reversible drug molecules with disulfide linker unit would be a promising candidate as proton pump antagonist to H⁺,K⁺-ATPase.

Otitis Media with Effusion (OME) in Urban Pediatric Population in a Tertiary Care Centre: A Clinical Study

Otitis media with effusion (OME) is a common condition affecting children. It is one of the most common causes for reduced hearing in pediatric age group leading to various learning disabilities including delayed speech development. The aim of this study was to find out various epidemiological characteristics and risk factors for developing OME and various treatment modalities depending on the clinical features and their outcomes in urban pediatric population. A prospective comparative study was done in 100 children taken 50 as cases and 50 as controls for a period of 2 years. The risk factors, common presenting features and the examination and investigational findings (tympanometry) of the study condition were compared among the cases and controls. Among the 50 cases, 28 children were treated medically and 22 underwent surgical treatment in the form of Myringotomy and Grommet insertion. The patients were followed up-to 6 months in both groups.

Optimization of beam dump shielding for K-130 cyclotron at VECC

A compact and efficient beam dump shield has been designed using Monte Carlo simulation code FLUKA to facilitate low background measurement of neutron and gamma rays using K130 cyclotron at Variable Energy Cyclotron Centre, Kolkata (VECC). Iron, lead and high density Polyethylene (HDPE) were considered in the design of the beam dump shield. Representative FLUKA simulation results have been validated using in-beam experiment performed on the same beam dump constituents. Experimental neutron and gamma-rays energy spectra have been found to be in fair agreement with the simulation results. Activation of various beam dump shield components were also carried out.

Generation and application of LET calibration curve for neutron dosimetry using CR-39 detector and microwave induced chemical etching

Microwave induced chemical etching (MICE) has been established as a faster and improved technique compared to other contemporary etching techniques for the development of tracks in a CR-39 detector. However, the methodology could not be applied for LET (linear energy transfer) spectrometry due to lack of a calibration curve using this method. For this purpose, a new LET calibration curve in the range of 12 keV/μm-799 keV/μm was generated considering different ions such as H, Li, C, O, and F on CR-39 having different LETs in water. An empirical relation was established from the obtained calibration curve for determining the value of LET (in water) from the value of V, the ratio of track etch rate to bulk etch rate. For application of this calibration curve in neutron dosimetry, CR-39 detectors were irradiated to neutrons generated from 120 and 142 MeV ¹⁶O+²⁷Al systems followed by a similar MICE procedure. The absorbed dose (D_LET) and the dose equivalent (H_LET) were obtained from the LET spectra and were found to be 13% and 10% higher for 142 MeV ¹⁶O+²⁷Al system than those for 120 MeV ¹⁶O+²⁷Al system, respectively. The outcome of the study demonstrates the possibility of using the MICE technique for neutron dose estimation by CR-39 via LET spectrometry.

Divalent ions are potential permeating blockers of the non-selective NaK ion channel: combined QM and MD based investigations

The interplay between the hydration energy barrier and optimum site-selectivity controls the permeation and blocking features of divalent metal ions.

Unbinding of fluorinated oxime drug from the AChE gorge in polarizable water: a well-tempered metadynamics study

A well-tempered metadynamics study reveals that fluorinated obidoxime is held more firmly in the AChE gorge in comparison to obidoxime.

Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions

Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7. The cation-π interactions in each of the protein-drug complexes are studied using distance, angle, a suitable functional form of them, and electrostatic criteria. The variation of cation-π functional is remarkably consistent with that of the Columbic variation. It is clearly observed that cation-π interactions for some of the residues in the catalytic active site (CAS) and peripheral anionic site (PAS) of the enzyme are either enhanced or reduced based on the nature of OP conjugation (i.e., nerve gas, tabun or pesticide, fenamiphos) when compared with the OP-free enzyme. The strength of cation-π interaction is strongly dependent on the type OP conjugation. The effect of conjugation at CAS is also seen to influence the cation-π interaction at the PAS region. The variation of cation-π interactions on the type of conjugating OP compounds might be suggestive of a reason as to why wide spectrum drug against any OP poisoning is yet to arrive in the market.

Effects of high neutron doses and duration of the chemical etching on the optical properties of CR-39

Effects of the duration of chemical etching on the transmittance, absorbance and optical band gap width of the CR-39 (Polyallyl diglycol carbonate) detectors irradiated to high neutron doses (12.7, 22.1, 36.0 and 43.5 Sv) were studied. The neutrons were produced by bombardment of a thick Be target with 12 MeV protons of different fluences. The unirradiated and neutron-irradiated CR-39 detectors were subjected to a stepwise chemical etching at 1h intervals. After each step, the transmission spectra of the detectors were recorded in the range from 200 to 900 nm, and the absorbances and optical band gap widths were determined. The effect of the etching on the light transmittance of unirradiated detectors was insignificant, whereas it was very significant in the case of the irradiated detectors. The dependence of the optical absorbance on the neutron dose is linear at short etching periods, but exponential at longer ones. The optical band gap narrows with increasing etching time. It is more significant for the irradiated dosimeters than for the unirradiated ones. The rate of the narrowing of the optical band gap with increasing neutron dose increases with increasing duration of the etching.

Selection of neutron-absorbing materials to improve the low-energy response of a Zr-based extended neutron monitor using Monte Carlo simulations

Monte Carlo simulations have been carried out using the FLUKA code to improve the neutron ambient dose equivalent [H*(10)] response of the ZReC (zirconium-lined portable neutron counter responding satisfactorily to neutrons up to 1 GeV) by introducing various neutron absorbers in the system such as cadmium, gadolinium, natural boron, enriched (10)B and borated polythene. It was found that ZReC can be effectively used as a portable neutron monitor by introducing any one of the following perforated layers: 5 mm thick natural boron, 0.5 mm thick enriched (10)B or 1 cm high-density polythene mixed with 50 % boron by weight. The integral response of the instrument was also calculated for some typical reference neutron fields. The relative ambient dose equivalent response of the said system is also found comparable with that of the existing LINUS neutron monitor.

An ultrafast molecular rotor based ternary complex in a nanocavity: a potential “turn on” fluorescence sensor for the hydrocarbon chain

Formation of a ternary complex by an ultrafast molecular rotor (UMR) with a macrocyclic cavitand has been investigated for the sensitive detection of the alkyl chain of a surfactant.

Neutron dose estimation via LET spectrometry using CR-39 detector for the reaction (9)Be (p, n)

CR-39 detectors, widely used for neutron dosimetry in accelerator radiation environment, have also been applied in tissue microdosimetry by generating the linear energy transfer (LET) spectrum. In this work, the neutron dose has been estimated via LET spectrometry for ⁹Be (p, n) reaction which is useful for personnel monitoring around particle accelerators and accelerator based therapy facilities. Neutrons were generated by the interaction of protons of 6 different energies from 4–24 MeV with a thick Be target. The LET spectra were obtained from the major and minor radii of each track and the thickness of removed surface. From the LET spectra, the absorbed dose (D_LET) and the dose equivalent (H_LET) were estimated using Q-L relationship as given by International Commission on Radiological Protection (ICRP) 60. The track density in CR-39 detector and hence the neutron yield was found to be increasing with the increase in projectile (proton) energy. Similar observations were also obtained for absorbed dose (D_LET) and dose equivalents (H_LET).

Deciphering the binding modes of hematoporphyrin to bovine serum albumin

Interaction of proteins with small molecules is important in understanding delivery and transport of different therapeutic agents, including drugs. In the present study, we investigated the interaction between hematoporphyrin (HP), the principal component of photosensitizing drug with bovine serum albumin (BSA) in aqueous buffer solution using UV-Vis absorption spectroscopy and fluorescence measurements. The results were further substantiated by molecular docking and molecular dynamics (MD) simulation. Our results revealed that fluorescence of BSA was dominantly quenched by the ground-state complex formation with HP accompanied by the electronic energy transfer (EET) to the later. We experimentally determined the thermodynamic parameters such as deltaG0, deltaH0, and deltaS0 for the HP-BSA system which were -35.5 kJ mole(-1), -56.4 kJ mole(-1) and -0.06 kJ mole(-1) K(-1), respectively. These parameters suggested hydrogen-bonding and Van der Waals forces playing major role in the complexation. This was also supported by the binding energy parameters calculated by molecular docking. Moreover, the experimentally determined deltaG0 nicely correlated with those determined by molecular docking and MD-simulation. Further, computational results clearly showed that the binding of HP with BSA in the subdomains IB and IIA.

Measurement of neutron spectra generated from bombardment of 4 to 24 MeV protons on a thick ⁹Be target and estimation of neutron yields

A systematic study on the measurement of neutron spectra emitted from the interaction of protons of various energies with a thick beryllium target has been carried out. The measurements were carried out in the forward direction (at 0° with respect to the direction of protons) using CR-39 detectors. The doses were estimated using the in-house image analyzing program autoTRAK_n, which works on the principle of luminosity variation in and around the track boundaries. A total of six different proton energies starting from 4 MeV to 24 MeV with an energy gap of 4 MeV were chosen for the study of the neutron yields and the estimation of doses. Nearly, 92% of the recoil tracks developed after chemical etching were circular in nature, but the size distributions of the recoil tracks were not found to be linearly dependent on the projectile energy. The neutron yield and dose values were found to be increasing linearly with increasing projectile energies. The response of CR-39 detector was also investigated at different beam currents at two different proton energies. A linear increase of neutron yield with beam current was observed.

Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics-umbrella sampling investigation

Because of the pivotal role that the nerve enzyme, acetylcholinesterase plays in terminating nerve impulses at cholinergic synapses. Its active site, located deep inside a 20 Å gorge, is a vulnerable target of the lethal organophosphorus compounds. Potent reactivators of the intoxicated enzyme are nucleophiles, such as bispyridinium oxime that binds to the peripheral anionic site and the active site of the enzyme through suitable cation-π interactions. Atomic scale molecular dynamics and free energy calculations in explicit water are used to study unbinding pathways of two oxime drugs (Ortho-7 and Obidoxime) from the gorge of the enzyme. The role of enzyme-drug cation-π interactions are explored with the metadynamics simulation. The metadynamics discovered potential of mean force (PMF) of the unbinding events is refined by the umbrella sampling (US) corrections. The bidimensional free energy landscape of the metadynamics runs are further subjected to finite temperature string analysis to obtain the transition tube connecting the minima and bottlenecks of the unbinding pathway. The PMF is also obtained from US simulations using the biasing potential constructed from the transition tube and are found to be consistent with the metadynamics-US corrected results. Although experimental structural data clearly shows analogous coordination of the two drugs inside the gorge in the bound state, the PMF of the drug trafficking along the gorge pathway point, within an equilibrium free energy context, to a multistep process that differs from one another. Routes, milestones and subtlety toward the unbinding pathway of the two oximes at finite temperature are identified.

Radiation mapping inside the bunkers of medium energy accelerators using a robotic carrier

The knowledge of ambient and peak radiation levels prevailing inside the bunkers of the accelerator facilities is essential in assessing the accidental human exposure inside the bunkers and in protecting sensitive electronic equipments by minimizing the exposure to high intensity mixed radiation fields. Radiation field mapping dynamically, inside bunkers are rare, though generally dose-rate data are available in every particle accelerator facilities at specific locations. Taking into account of the fact that the existing neutron fields with a spread of energy from thermal up to the energy of the accelerated charged projectiles, prompt photons and other particles prevailing during cyclotron operation inside the bunkers, neutron and gamma survey meters with extended energy ranges attached to a robotic carrier have been used. The robotic carrier movement was controlled remotely from the control room with the help of multiple visible range optical cameras provided inside the bunkers and the wireless and wired protocols of communication helped its movement and data acquisition from the survey meters. Variable Energy Cyclotron Centre, Kolkata has positive ion accelerating facilities such as K-130 room Temperature Cyclotron, K-500 Super Conducting Cyclotron and a forthcoming 30 MeV Proton Medical Cyclotron with high beam current. The dose rates data for K-130 Room Temperature Cyclotron, VECC were collected for various energies of alpha and proton beams losing their total energy at different stages on different materials at various strategic locations of radiological importance inside the bunkers. The measurements established that radiation levels inside the machine bunker dynamically change depending upon the beam type, beam energy, machine operation parameters, deflector condition, slit placement and central region beam tuning. The obtained inference from the association of dose rates with the parameters like beam intensity, type and energy of projectiles, helped in improving the primary beam transmission and minimizing the ambient radiation fields inside the bunkers.

Energetics of Ortho-7 (oxime drug) translocation through the active-site gorge of tabun conjugated acetylcholinesterase

Oxime drugs translocate through the 20 Å active-site gorge of acetylcholinesterase in order to liberate the enzyme from organophosphorus compounds' (such as tabun) conjugation. Here we report bidirectional steered molecular dynamics simulations of oxime drug (Ortho-7) translocation through the gorge of tabun intoxicated enzyme, in which time dependent external forces accelerate the translocation event. The simulations reveal the participation of drug-enzyme hydrogen bonding, hydrophobic interactions and water bridges between them. Employing nonequilibrium theorems that recovers the free energy from irreversible work done, we reconstruct potential of mean force along the translocation pathway such that the desired quantity represents an unperturbed system. The potential locates the binding sites and barriers for the drug to translocate inside the gorge. Configurational entropic contribution of the protein-drug binding entity and the role of solvent translational mobility in the binding energetics is further assessed.

Anterior tibial artery perforator plus flaps for reconstruction of post-burn flexion contractures of the knee joint

Background. Post-burn flexion contractures of the knee may arise even with adequate treatment of the burn injury. After release of the contracture, most of these defects require flap coverage. Here we describe the application of the perforator plus flap concept in the management of these contractures. Method. Between December 2010 and December 2011 five female and two male patients with knee contractures were operated on using a perforator plus flap from the anterior tibia artery perforator. In one patient both sides were operated on and the rest had unilateral surgeries. All patients had mature scars and the aetiology was thermal burn injury. All these contractures were categorized as Category 4 and Level 3 by the ICIDH guidelines with an average contracture angle of 87.5 degrees. The flap was raised after release of the defect and a Doppler study located the perforator below the fibular head. The base of the flap was kept intact at all times. The flap was then transposed towards the defect and inset in a tensionless manner. Results. All flaps survived well with marginal necrosis in only one flap, providing stable coverage to the knee joint. The average residual contracture was around 10 degrees and the average range of flexion was 10-120 degrees. Conclusion. The perforator plus flap can be an excellent choice in defects over the posterior aspect of the knee where important neurovascular structures and tendons are exposed.

LEVEL OF EVIDENCE

Level IV.

Directional distribution of the ambient neutron dose equivalent from 145-MeV ¹⁹F projectiles incident on thick Al target

The directional distribution of the ambient neutron dose equivalent from 145-MeV (19)F projectiles bombarding a thick aluminium target is measured and analysed. The measurements are carried out with a commercially available dose equivalent meter at 0°, 30°, 60° and 90° with respect to the beam direction. The experimental results are compared with calculated doses from EMPIRE nuclear reaction code and different empirical formulations proposed by others. The results are also compared with the measured data obtained from an earlier experiment at a lower projectile energy of 110 MeV for the same target-projectile combination.