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When biomedical crises strike, structural biologists worldwide respond by determining the structures of relevant proteins and their complexes, resulting in an avalanche of data that can be overwhelming without a resource designed to classify, annotate and validate them. An advanced information system is necessary to extract and infer knowledge from a deluge of uncurated and disjointed data and publications., As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.

The structure of serum albumin in complex with dexamethasone reveals why the drug may not always help COVID-19 patients., Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Here, the first structure of serum albumin in complex with dexamethasone is reported. Dexamethasone binds to drug site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with an analysis of publicly available clinical data from Wuhan and suggests that an adjustment of the dexamethasone regimen should be further investigated as a strategy for patients affected by two major COVID-19 risk factors: low albumin levels and diabetes.

The current-voltage curves of a double strand DNA nanowire connected to armchair graphene nanoribbon leads are investigated using the tight-binding Hamiltonian model and the Landauer-Buttiker formalism. The nonlinear behavior of the current-voltage for different lengths of the DNA nanowire is calculated and interpreted through the corresponding density of states and transmission probability. The behavior of the current-voltage changes as the temperature or width of the leads varies and is also affected by the randomization of parallel and perpendicular hopping terms in the DNA. Around zero bias of the leads, the current-voltage depends on the dimerization effects of parallel hopping in the device.

The possibility of the s-wave superconductive state in armchair graphene nanoribbons is studied within the attractive Hubbard model, standard BCS theory, and Green’s function approach. Bogoliubov de Gennes equations are derived for this system in the singlet state. A nonzero critical temperature is found which depends on the width of the system. This critical temperature decreases as the width of the system increases and for sufficiently large widths, its value reaches a constant amount which could be taken as the critical temperature of the graphene sheet. The critical temperature also depends on band-filling which, around half band-filling, shows a maximum. However, at half-filling, it drops to a lower value less than its maximum.

In the framework of the Green's functions approach, random tight-binding model and using the coherent potential approximation, electronic characteristics of the bilayer graphene are investigated by exploring various forms of substitutional doping of a single or both layers of the system by either boron and (or) nitrogen atoms. The results for displacement of the Fermi level resemble the behavior of acceptor or donor doping in a conventional semiconductor, dependent on the impurity type and concentration. The particular pattern of doping of just one layer with one impurity type is most efficient for opening a gap within the energy bands which could be tuned directly by impurity concentration. Doping both layers at the same time, each with one impurity type, leads to an anomaly whereby the gap decreases with increasing impurity concentration.

The Kubo formula is used to extract the electrical conductivity (EC) of different diameters of doped zigzag carbon nanotubes and their corresponding unzipped armchair graphene nanoribbons, as a function of temperature and chemical potential, within the tight-binding Hamiltonian model and Green's functions approach. The results reveal more sensitivity to temperature for semiconducting systems in addition to a decrease in EC of all systems with increasing cross-sections.

Through the Green's function formalism and tight-binding Hamiltonian model calculations, the temperature dependent electronic thermal conductivity (TC) for different diameters of zigzag carbon nanotubes and their corresponding unzipped armchair graphene nanoribbons is calculated. All functional temperature dependencies bear crossovers, for which, at higher temperatures, nanotubes have a slightly higher TC than their derived nanoribbons, while below that crossover, both systems exhibit a significant coincidence over a moderate range of lower temperatures. Noticeably, TC decreases with increasing the width or diameter of the corresponding systems. Also, at low temperatures TC is proportional to the density of states around the Fermi level, and thus increasing for metal or semiconductors of narrower gap cases.

The band structure, density of states (DOS), and electrical conductivity (EC) of different configurations of a double-strand poly-GC-poly-AT DNA-like nanowire are investigated within the tight-binding Hamiltonian model and the Green's function formalism. Three different configurations of the double-strand DNA-like nanowire were considered: infinite, finite, and cyclic. The change of behavior in the band structure due to the introduction of dimerization effects of the longitudinal hopping terms was studied. Without dimerization, the DNA-like nanowire behaves as a conductor and with dimerization, a semiconductor behavior was observed. This behavior change was also verified through the calculation of the DOS via the Green's function formalism. The effects of the finite size of the DNA-like nanowire and also the effect of length increase on the EC of the system were studied using Kubo formula. There exists a direct relationship between EC and length of DNA-like nanowire. As length increases, so does the EC of the DNA-like nanowire. This information can be useful in both theoretical research and experimental development of DNA-based molecular electronics.

We examine a magnetic moment subject to a static external magnetic field and a time dependent driving magnetic field. Taking the system in the highly anisotropic limit, like that of a thin film, we lower the complexity of the system so that it may be analyzed for transitions to chaos analytically using the Melnikov method. Guided by the calculation of the Melnikov bifurcation functions we computationally calculated the Lyapunov characteristic exponents for several lines in parameter space and find that the Melnikov method is a good predictor of chaotic motion for sufficiently small external fields. Motion plots and Poincare sections are also plotted for several parameter space points to observe the transitions to and from chaos around the calculated Melnikov bifurcations functions.

The electronic behavior of the long disordered DNA nanowires in both dry and wet conditions is investigated through the band structure and density of states of a tight-binding Hamiltonian model for π-electrons of the backbone, using Green׳s functions approach. For a chosen set of parameters in the dry case, semiconducting behavior is reproduced. It is also shown that for sufficiently long strands, the order of the base pairs has no noticeable effect on the energy band-gap. Moreover, this semiconducting duplex shows metallic tendencies when interacting with the environment of polar molecules.

We show here how to create macroscopic quantum states in a semiconductor device: a chain of InAs quantum dots embedded in an InP nanowire. Filling the nanowire with 4 electrons per dot creates a synthetic spin-one chain, with four-fold degenerate topological ground state protected by a Haldane gap. The four states correspond to two spin-½ quasiparticles localised at the ends of the macroscopic wire. The quasiparticle spins are mapped onto a robust, macroscopic, singlet-triplet qubit. These predictions are supported by a microscopic theory and extensive numerical simulations.

It has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new crystal structure should deposit their primary experimental data (X-ray diffraction images) to one of the dedicated resources created in recent years. Here, we describe our experiences developing the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC) and describe several examples of a crucial role that diffraction data can play in improving previously determined protein structures. In its first four years, several hundred crystallographers have deposited data from over 5200 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing. Preliminary analysis indicates that about 95% of the archived data can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of using the automated metadata extraction and automated processing as a validation step for the deposition of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles.

The Landau–Lifshitz–Gilbert equation is analyzed in the case of a configuration involving easy plane isotropy under the influence of a sinusoidally oscillating magnetic field and a demagnetizing field. Through the use of numerical techniques, chaotic behavior is found and analyzed. By reducing the system to a discrete map (numerically), bifurcation diagrams for the system are computed. The system is found to exhibit a period doubling cascade route to chaos, and it obeys certain convergence rules for chaotic transitions outlined by Feigenbaum. A connection is drawn between the route to chaos and the geometry of the system, and comparisons are made with similar systems. Within the chaotic regime, windows of arbitrarily large period are suspected to exist, and explicitly illustrated and discussed for a period three window.

We examine the motion of a spin subject to a static external field, dynamic demagnetizing fields, and a relatively weak oscillatory driving field. More specifically, we study the initial transient behavior just after all these fields are turned on and present analytic calculations based on an approximation scheme for the motion of the spin. We find that two modes – a mode at the driving frequency and a mode at the natural resonant frequency – play an important role in the initial transient. Because of the nonlinear nature of the spin equations of motion, one also finds, only in the initial transient, modes with doubled frequencies of the initial two modes and modes involving the sum and difference frequencies of the initial two modes. We also examine large amplitude transients in specific cases through numerical calculations.

The isochorismate synthase DhbC from Bacillus anthracis is essential for the biosynthesis of the siderophore bacillibactin by this pathogenic bacterium. The structure of the selenomethionine-substituted protein was determined to 2.4 Å resolution using single-wavelength anomalous diffraction. B. anthracis DhbC bears the strongest resemblance to the Escherichia coli isochorismate synthase EntC, which is involved in the biosynthesis of another siderophore, namely enterobactin. Both proteins adopt the characteristic fold of other chorismate-utilizing enzymes, which are involved in the biosynthesis of various products, including siderophores, menaquinone and tryptophan. The conservation of the active-site residues, as well as their spatial arrangement, suggests that these enzymes share a common Mg(2+)-dependent catalytic mechanism.

We present a theory of the electronic properties of gated graphene nanoribbon rings with zigzag edges in Möbius and cylindrical configurations. The finite width opens a gap and nontrivial topology of the Möbius ring leads to a single edge with edge states with an induced, effective gauge field, in analogy to topological insulators. The single zigzag edge leads to a shell of degenerate states at the Fermi level and a ferromagnetic (FM) ground state at half-filling, i.e., at charge neutrality, due to electron-electron interactions. For fractional fillings, both the magnetic moment and the energy gap are found to oscillate as a function of the shell filling. In cylindrical rings, the two edges lead to AF ground state at half-filling but FM ground state at fractional fillings., NSERC; NRC; Canadian Institute for Advanced Research; UCCS-CRCW

Anabolic ornithine transcarbamoylase (aOTC) catalyzes the reaction between carbamoyl phosphate (CP) and L-ornithine (ORN) to form L-citrulline and phosphate in the urea cycle and L-arginine biosynthesis. The crystal structure of unliganded aOTC from Campylobacter jejuni (Cje aOTC) was determined at 2.7 Å resolution and refined to an R(work) of 20.3% and an R(free) of 24.0%. Cje aOTC is a trimer that forms a head-to-head pseudohexamer in the asymmetric unit. Each monomer is composed of an N-terminal CP-binding domain and a C-terminal ORN-binding domain joined by two interdomain helices. The Cje aOTC structure presents an open conformation of the enzyme with a relatively flexible orientation of the ORN-binding domain respective to the CP-binding domain. The conformation of the B2-H3 loop (residues 68-78), which is involved in binding CP in an adjacent subunit of the trimer, differs from that seen in homologous proteins with CP bound. The loop containing the ORN-binding motif (DxxxSMG, residues 223-230) has a conformation that is different from those observed in unliganded OTC structures from other species, but is similar to those in structures with bound ORN analogs. The major differences in tertiary structure between Cje aOTC and human aOTC are described.

The LabDB laboratory information management system (LIMS) tracks, organizes and analyzes data from chemical and solution management, protein production, crystallization, diffraction, structure solution, and in vitro biochemical and biophysical experiments. The system is comprised of multiple modules specialized for different tasks, such as the Xtaldb system for crystallization or the hkldb module of the HKL-3000 suite for diffraction data collection and structure solution. The biochemical/biophysical experiments tracked by LabDB include spectrophotometric binding and kinetics, thermal shift binding, isothermal titration calorimetry (ITC) and protein quantitation. These tools associate functional and structural experiments, for example, for selecting likely substrates for co-crystallization and soaking experiments. Whenever possible, the system harvests data with no or minimal user intervention from laboratory hardware. Devices that may connect to or import data into LabDB include crystal observation (Rigaku Minstrel HT and Formulatrix Rock Imager), liquid handling (Formulatrix Rock Maker and Emerald Opti-Matrix Maker), chromatography (GE Healthcare AKTA), quantitation (Caliper LabChip GX II and Bio-Rad Gel Doc EZ), RT-PCR (Applied Biosystems 7900HT and Bio-Rad C1000/CFX96) and ITC (MicroCal iTC-200) systems. LabDB is used by two high-throughput PSI:Biology centers (MCSG and NYSGRC) as well as other major NIH consortia (the Center for Structural Genomics of Infectious Diseases and the Enzyme Function Initiative), and track millions of experiments on tens of thousands of targets.[1] The system also provides extensive data mining and analysis tools for translating raw experimental data into information and knowledge. We present examples of analyses generated by the system useful in designing new experiments.

We investigate the tunneling of carriers in a quasi-one-dimensional array of semimagnetic quantum dots. The large magnetopolaron effects due to the exchange interaction of carriers with magnetic ions result in a transmission via solitonlike electronic states. The intensity-dependent transmission coefficient shows the opening of intensity-dependent gaps in the transmission spectrum.

We consider a superlattice built of an array of narrow layers of a narrow gap material (quantum wells) sandwiched hy thick layers of a wide gap material (barriers). The electromagnetic wave with frequency below the band gap of the wells results in optical nonlinearities confined to narrow layers. We model this system by an array of equally spaced, infinitesimally thin layers. characterized by Kerr nonlinearity. It is shown that the electromagnetic wave induces intensity dependent gaps in the spectrum giving rise to a multivalued transmission coefficient. The origin of gaps, their connection to chaos, and a possible application for bistable devices are discussed.

We investigate electronic states and the far-infrared absorption spectrum of a two-dimensional (2D) hydrogenic impurity in a parabolic quantum wire in a magnetic field. The problem is mapped into the problem of interacting nonlinear harmonic oscillators. The evolution of the energy levels and level statistics from a 2D to a 1D effective hydrogen atom is investigated in the quantum and classically chaotic regimes. The ground-state energy reflects a delicate balance between a blueshift due to confinement and a redshift due to an increase in binding energy. In the absence of a magnetic field, the model reduces to the well-known problem of quantum chaos in a 3D hydrogen atom in a magnetic field in a zero angular-momentum channel. The presence of a magnetic field in the wire breaks the scaling behavior inherent in the 3D hydrogen problem.

A possible novel mechanism for superconductivity in heavy fermion systems is proposed. The Coqblin-Schrieffer model for a Kondo-like impurity is studied in the limit of large spin degeneracy. The effective dynamical interaction between conduction electrons mediated by spin fluctuations is calculated and shown to be attractive at finite frequencies.

We consider a semiconductor superlattice built of quasi-two-dimensional layers of narrow-band-gap material sandwiched by barriers of wide-band-gap material. We show that when the electromagnetic wave with frequency below the band gap of the superlattice propagates along the superlattice axis, it induces intensity-dependent gaps in the spectrum. The connection between these unusual gaps and spatial chaos is explored. The possibility of bistable devices is discussed.