Nanografting de novo proteins onto gold surfaces

The immobilization of novel proteins onto addressable locations on a flat surface has potential applications in a range of biotechnologies. Here we describe the nanopatterning of a de novo protein onto a gold surface. Patterning was achieved using a technique called nanografting, in which the tip of an atomic force microscope is used to disrupt a preexisting monolayer of alkanethiol molecules on a gold surface, thereby facilitating exchange with alternative thiol-linked molecules from the surrounding solution. The protein used for these studies was chosen from a designed combinatorial library of de novo sequences expressed in E. coli and was engineered to have a glycine-glycine-cysteine tag at its C-terminus, thereby enabling attachment to the gold surface through a single cysteine thiol. The average height of the grafted protein patterns was found to be somewhat higher than expected from the known NMR structure of the protein. Compression of the nanografted patches by an external force (below 10 nN) was reversible but showed some hysteresis. Interestingly, both the energy required to deform the immobilized protein patterns and the energy defined by the hysteresis loop were found to be of the same order as the energy required to unfold the monomeric protein in solution. These studies demonstrate the possibility of preparing nanometer scale protein arrays, lowering significantly the volume requirements of the protein samples necessary to fabricate protein-based biosensor arrays and thereby providing a base for increasing their sensitivity.     

A study on natural coral stone—a fractal solid

This present research work contains the study of natural fractal material, coral stone. X-ray diffraction, FTIR, optical, DC and AC electrical characteristics are studied. The study includes Arrhenius like plots for both wafer and powder form of the material. Measurements show a possible partially irreversible phase transition occurs when coral is heated for a long time at an about 115?°C. From the XRD data it has been also established that coral stone contains nano sized clusters which is supported by DC electrical measurement. The variation of AC conductivity of coral with thickness of the sample is studied and found exhibit an interesting feature of fractal solid. A scaling relation between AC conductivity and thickness has also been proposed here. The overall behavior of the specimen is like that of a fractal system.     

Chemical Route to Twisted Graphene,Graphene Oxide and Boron Nitride

The recently discovered twisted graphene has attracted considerable interest. A simple chemical route was found to prepare twisted graphene by covalently linking layers of exfoliated graphene containing surface carboxyl groups with an amine-containing linker (trans-1,4-diaminocyclohexane). The twisted graphene shows the expected selected area electron diffraction pattern with sets of diffraction spots out with different angular spacings, unlike graphene, which shows a hexagonal pattern. Twisted multilayer graphene oxide could be prepared by the above procedure. Twisted boron nitride, prepared by cross-linking layers of boron nitride (BN) containing surface amino groups with oxalic acid linker, exhibited a diffraction pattern comparable to that of twisted graphene. First-principles DFT calculations threw light on the structures and the nature of interactions associated with twisted graphene/BN obtained by covalent linking of layers.     

Ultra-thin layer MALDI mass spectrometry of membrane proteins in nanodiscs

Nanodiscs have become a leading technology to solubilize membrane proteins for biophysical, enzymatic, and structural investigations. Nanodiscs are nanoscale, discoidal lipid bilayers surrounded by an amphipathic membrane scaffold protein (MSP) belt. A variety of analytical tools has been applied to membrane proteins in nanodiscs, including several recent mass spectrometry studies. Mass spectrometry of full-length proteins is an important technique for analyzing protein modifications, for structural studies, and for identification of proteins present in binding assays. However, traditional matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry methods for analyzing full-length membrane proteins solubilized in nanodiscs are limited by strong signal from the MSP belt and weak signal from the membrane protein inside the nanodisc. Herein, we show that an optimized ultra-thin layer MALDI sample preparation technique dramatically enhances the membrane protein signal and nearly completely eliminates the MSP signal. First-shot MALDI and MALDI imaging are used to characterize the spots formed by the ultra-thin layer method. Furthermore, the membrane protein enhancement and MSP suppression are shown to be independent of the type of membrane protein and are applicable to mixtures of membrane proteins in nanodiscs.     

A Single‐Molecule‐Level Mechanistic Study of Pd‐Catalyzed and Cu‐Catalyzed Homocoupling of Aryl Bromide on an Au(111) Surface

On‐surface Pd‐ and Cu‐catalyzed C?C coupling reactions between phenyl bromide functionalized porphyrin derivatives on an Au(111) surface have been investigated under ultra‐high vacuum conditions by using scanning tunneling microscopy and kinetic Monte Carlo simulations. We monitored the isothermal reaction kinetics by allowing the reaction to proceed at different temperatures. We discovered that the reactions catalyzed by Pd or Cu can be described as a two‐phase process that involves an initial activation followed by C?C bond formation. However, the distinctive reaction kinetics and the C?C bond‐formation yield associated with the two catalysts account for the different reaction mechanisms: the initial activation phase is the rate‐limiting step for the Cu‐catalyzed reaction at all temperatures tested, whereas the later phase of C?C formation is the rate‐limiting step for the Pd‐catalyzed reaction at high temperature. Analysis of rate constants of the Pd‐catalyzed reactions allowed us to determine its activation energy as (0.41±0.03) eV.     

Current-induced decoherence in the multichannel Kondo problem

The properties of a local spin S=1/2 coupled to K independent wires is studied in the presence of bias voltages which drive the system out of thermal equilibrium. For K?1, a perturbative renormalization group approach is employed to construct the voltage-dependent scaling function for the conductance and the T matrix. In contrast to the single-channel case, the Kondo resonance is split even by bias voltages small compared to the Kondo temperature T(K), V?T(K). Besides the applied voltage V, the current-induced decoherence rate Γ?V controls the physical properties of the system. While the presence of V changes the structure of the renormalization group considerably, decoherence turns out to be very effective in prohibiting the flow towards new nonequilibrium fixed points even in variants of the Kondo model where currents are partially suppressed.     

Virtual-site correlation mean field approach to criticality in spin systems

We propose a virtual-site correlation mean field theory for dealing with interacting many-body systems. It involves a coarse-graining technique that terminates a step before the mean field theory: While mean field theory deals with only single-body physical parameters, the virtual-site correlation mean field theory deals with single- as well as two-body ones, and involves a virtual site for every interaction term in the Hamiltonian. We generalize the theory to a cluster virtual-site correlation mean field, that works with a fundamental unit of the lattice of the many-body system. We apply these methods to interacting Ising spin systems in several lattice geometries and dimensions, and show that the predictions of the onset of criticality of these models are generally much better in the proposed theories as compared to the corresponding ones in mean field theories.     

Ultracold atomic gases in optical lattices: mimicking condensed matter physics and beyond

We review recent developments in the physics of ultracold atomic and molecular gases in optical lattices. Such systems are nearly perfect realisations of various kinds of Hubbard models, and as such may very well serve to mimic condensed matter phenomena. We show how these systems may be employed as quantum simulators to answer some challenging open questions of condensed matter, and even high energy physics. After a short presentation of the models and the methods of treatment of such systems, we discuss in detail, which challenges of condensed matter physics can be addressed with (i) disordered ultracold lattice gases, (ii) frustrated ultracold gases, (iii) spinor lattice gases, (iv) lattice gases in “artificial” magnetic fields, and, last but not least, (v) quantum information processing in lattice gases. For completeness, also some recent progress related to the above topics with trapped cold gases will be discussed.

Motto:     

Time-Reversibility,Causality and Compression-Complexity

Detection of the temporal reversibility of a given process is an interesting time series analysis scheme that enables the useful characterisation of processes and offers an insight into the underlying processes generating the time series. Reversibility detection measures have been widely employed in the study of ecological, epidemiological and physiological time series. Further, the time reversal of given data provides a promising tool for analysis of causality measures as well as studying the causal properties of processes. In this work, the recently proposed Compression-Complexity Causality (CCC) measure (by the authors) is shown to be free of the assumption that the "cause precedes the effect", making it a promising tool for causal analysis of reversible processes. CCC is a data-driven interventional measure of causality (second rung on the Ladder of Causation) that is based on Effort-to-Compress (ETC), a well-established robust method to characterize the complexity of time series for analysis and classification. For the detection of the temporal reversibility of processes, we propose a novel measure called the Compressive Potential based Asymmetry Measure. This asymmetry measure compares the probability of the occurrence of patterns at different scales between the forward-time and time-reversed process using ETC. We test the performance of the measure on a number of simulated processes and demonstrate its effectiveness in determining the asymmetry of real-world time series of sunspot numbers, digits of the transcedental number π and heart interbeat interval variability.     

Chemical Features and Therapeutic Applications of Curcumin (A Review)

Russian Journal of General Chemistry - Curcumin, a component of the “Golden Spice” turmeric, has been recognized for its medicinal importance since ancient times. It can be isolated...