All-atom de novo protein folding with a scalable evolutionary algorithm

The search for efficient and predictive methods to describe the protein folding process at the all-atom level remains an important grand-computational challenge. The development of multi-teraflop architectures, such as the IBM BlueGene used in this study, has been motivated in part by the large computational requirements of such studies. Here we report the predictive all-atom folding of the forty-amino acid HIV accessory protein using an evolutionary stochastic optimization technique. We implemented the optimization method as a master-client model on an IBM BlueGene, where the algorithm scales near perfectly from 64 to 4096 processors in virtual processor mode. Starting from a completely extended conformation, we optimize a population of 64 conformations of the protein in our all-atom free-energy model PFF01. Using 2048 processors the algorithm predictively folds the protein to a near-native conformation with an RMS deviation of 3.43 A in < 24 h.     

Highly reduced, polyoxo(alkoxo)vanadium(III/IV) clusters

A family of high nuclearity oxo(alkoxo)vanadium clusters in unprecedentedly low oxidation states is reported, synthesised from simple vanadium diketonate precursors in alcohols under solvothermal conditions. Crystal structures of [V18(O)12(OH)2(H2O)4(EtO)22(O2CPh)6(acac)2] (1), [V16Na2(O)18(EtO)16(EtOH)2(O2CPh)6(HO2CPh)2]infinity (2), [V13(O)13(EtO)15(EtOH)(RCO2)3] in which R=adamantyl (3) or Ph3C (4), and [V11(O)12(EtO)13(EtOH)(Ph3CCO2)2(MePO3)] (5) are reported, revealing these to be {VIII 16VIV 2} (1), {VIII 9VIV 3VV} (3 and 4) and {VIII 3VIV 8} (5) clusters, while 2 consists of isolated {VIII 8VIV 8} clusters bridged into polymeric chains by {Na2(OEt)2} fragments. Solvothermal conditions are essential to the formation of these species, and the level of oxidation of the isolated clusters is in part controlled by the crystallisation time, with the lowest mean-oxidation-state species being isolated by direct crystallisation on controlled cooling of the reaction solutions.     

A photoprogrammable electronic nose with switchable selectivity for VOCs using MOF films

Advanced analytical applications require smart materials and sensor systems that are able to adapt or be configured to specific tasks. Based on reversible photochemistry in nanoporous materials, we present a sensor array with a selectivity that is reversibly controlled by light irradiation. The active material of the sensor array, or electronic nose (e-nose), is based on metal–organic frameworks (MOFs) with photoresponsive fluorinated azobenzene groups that can be optically switched between their trans and cis state. By irradiation with light of different wavelengths, the trans–cis ratio can be modulated. Here we use four trans–cis values as defined states and employ a four-channel quartz-crystal microbalance for gravimetrically monitoring the molecular uptake by the MOF films. We apply the photoprogrammable e-nose to the sensing of different volatile organic compounds (VOCs) and analyze the sensor array data with simple machine-learning algorithms. When the sensor array is in a state with all sensors either in the same trans- or cis-rich state, cross-sensitivity between the analytes occurs and the classification accuracy is not ideal. Remarkably, the VOC molecules between which the sensor array shows cross-sensitivity vary by switching the entire sensor array from trans to cis. By selectively programming the e-nose with light of different colors, each sensor exhibits a different isomer ratio and thus a different VOC affinity, based on the polarity difference between the trans- and cis-azobenzenes. In such photoprogrammed state, the cross-sensitivity is reduced and the selectivity is enhanced, so that the e-nose can perfectly identify the tested VOCs. This work demonstrates for the first time the potential of photoswitchable and thus optically configurable materials as active sensing material in an e-nose for intelligent molecular sensing. The concept is not limited to QCM-based azobenzene-MOF sensors and can also be applied to diverse sensing materials and photoswitches.

A sensor array with four identical photoresponsive azobenzene-containing metal–organic framework films is selectively irradiated. By photoprogamming the array, the sensor selectivity is switched and optimized.     

A mechanistic study of Protein A chromatography resin lifetime

A mechanistic study into Protein A chromatographic resin lifetime limitations is presented. Binding and mass transport properties of two widely used agarose-based Protein A resins were studied to distinguish between the roles of resin fouling due to product/impurity build-up and ligand degradation as contributory factors towards the decline in binding capacity with use. Cycling studies were conducted with and without product loading on the columns to separate out the influence of resin fouling. Ligand degradation under the mildly alkaline conditions used for column regeneration was determined to be the primary cause for Protein A resin capacity decline with usage. The use of lower concentrations of caustic and the use of stabilizing excipients to protect the Protein A ligand during cleaning and sanitization were found to be useful techniques in maintaining column performance. The results presented in this paper provide a clearer understanding of the causative factors that limit Protein A chromatographic resin lifetime. It is anticipated that these findings will assist in the development of more robust and economical downstream manufacturing processes for monoclonal antibody and Fc fusion protein purification.     

Supersymmetry, PT-symmetry and spectral bifurcation

We demonstrate that large class of PT-symmetric complex potentials, which can have isospectral real partner potentials, possess two different superpotentials. In the parameter domain, where the superpotential is unique, the spectrum is real and shape-invariant, leading to translational shift in a suitable parameter by real units. The case of two different superpotentials, leading to same potential, yields broken PT-symmetry, the energy spectra in the two phases being separated by a bifurcation. Interestingly, these two superpotentials generate the two disjoint sectors of the Hilbert space. In the broken case, shape invariance produces complex parametric shifts.     

Inhomogeneous Heisenberg spin chain and quantum vortex filament as non-holonomically deformed NLS systems

Through the Hasimoto map, various dynamical systems can be mapped to different integrodifferential generalizations of Nonlinear Schrödinger (NLS) family of equations some of which are known to be integrable. Two such continuum limits, corresponding to the inhomogeneous XXX Heisenberg spin chain [J. Phys. C 15, L1305 (1982)] and that of a thin vortex filament moving in a superfluid with drag [Eur. Phys. J. B 86, 275 (2013) 86; Phys. Rev. E 91, 053201 (2015)], are shown to be particular non-holonomic deformations (NHDs) of the standard NLS system involving generalized parameterizations. Crucially, such NHDs of the NLS system are restricted to specific spectral orders that exactly complements NHDs of the original physical systems. The specific non-holonomic constraints associated with these integrodifferential generalizations additionally posses distinct semi-classical signature.     

A new computational method for solving fully fuzzy linear systems of triangular fuzzy numbers

In this paper, a new computational method is proposed to solve fully fuzzy linear systems (FFLS) of triangular fuzzy numbers based on the computation of row reduced echelon form for solving the crisp linear system of equations. The method is illustrated by solving three numerical examples. As compared to the existing methods, the proposed method is easy to understand and to apply for solving FFLS occurring in real life situations and scientific applications. The primary advantage of the proposed method is that, by using it, the consistency of the FFLS can be checked easily and nature of the solutions of an FFLS can also be obtained which may be unique or infinite.     

Tertiary phosphine-appended transition metal ferrocenyl dithiocarbamates: Syntheses,Hirshfeld surface,and electrochemical analyses

Five new heteroleptic complexes of Cu(I), Ag(I), and Ni(II) having formulae [Cu₃(dtc)₂(dppf)₂]PF₆ ( Cu-I ), [Cu₃(dtc)₂(dppe)₂]PF₆ ( Cu-II ), [Cu(PPh₃)₂(dtc)] ( Cu-III ), [Ag₃(dtc)₂(PPh₃)₂]NO₃ ( Ag-I ), and [Ni(dtc)(dppf)]PF₆ ( Ni-I ) (dtc = N-ethanol-N-methylferrocenyl-dithiocarbamate; dppf = 1,1′-bis(diphenylphosphino)ferrocene; dppe = 1,1′-bis(diphenylphosphino)ethane; PPh₃ = tripheylphosphine) have been synthesized and characterized using elemental analysis, Fourier-transform infrared, multinuclear nuclear magnetic resonance, UV–Vis spectroscopy, and single-crystal X-ray diffraction. The single-crystal X-ray diffraction studies indicate that Ag-I forms a rare trinuclear cluster in which the geometry around the two silver centers Ag1 and Ag3 is distorted tetrahedral, whereas the third silver center Ag2 shows a distorted trigonal planar geometry. The Ni-I complex has a distorted square-planar geometry around the Ni center. In addition, a side product [Ag₂{S₂(dppf)₂}] ( Ag-II ) was obtained during an attempt to synthesize [Ag(dppf)(dtc)], where the two Ag centers are bridged by two sulfido centers and coordinated with two phosphorus centers of the dppf ligand to give rise to a distorted tetrahedral geometry. The solid-state structures of Ag-I , Ni-I , and Ag-II are stabilized by a variety of weak interactions. The nature of these interactions has been addressed with the help of Hirshfeld surface analyses. In addition, the weak argentophilic interaction in Ag-I and Ag-II have been studied using quantum theory of atoms in molecules and natural bond orbital calculations. The electrochemical properties of the complexes have been investigated using cyclic voltammetry, where Cu-I and Cu-II exhibited two quasi-reversible waves, whereas Cu-III , Ag-I , Ag-II , and Ni-I exhibited only one quasi-reversible peak.     

Ferrocene‐substituted bis(ethynyl)anthracene compounds as anticancer agents

Three compounds ( 1 – 3 ) were synthesized, where ethynylferrocene is substituted at different positions of anthracene and anthraquinone, and their biological properties were investigated. Compounds 1 – 3 were characterized using NMR and mass spectroscopies and confirmed by their single‐crystal X‐ray structure. They were also characterized from electronic and photophysical properties. All three crystal structures were optimized using density functional theory calculations. The presence of C–H???π interactions in 1 – 3 leads to the formation of two‐ and three‐dimensional networks. The bioactivity of 1 – 3 was expressed by molecular docking with various cancerous proteins, which participated in progression of cancer. Compound 2 displayed the best interaction with cancer‐related Aurora A protein in terms of both binding energy (?10.61 kcal mol^?1) as well as inhibition constant (16.74 nM). The molecular docking result also coincides with cytotoxicity on cancer cell lines (A375, HeLa) and DNA/protein binding affinity.