A single point mutation disrupts the capsid assembly in Sesbania Mosaic Virus resulting in a stable isolated dimer

Protein-protein interactions play a Crucial role in Virus assembly and stability. With the view of disrupting capsid assembly and capturing smaller oligomers, interfacial residue mutations were carried Out in the coat protein gene of Sesbania Mosaic Virus, a T=3 ss (+) RNA plant virus. A single point mutation of a Trp 170 present at the five-fold interface of the virus to a charged residue (Glu or Lys) arrested assembly of virus like particles and resulted in stable Soluble dimers of the capsid Protein. The X-ray crystal structure of one of the isolated dimer mutants - rCP Delta N65W170K was determined to a resolution of 2.65 angstrom. Detailed analysis of the dimeric mutant protein structure revealed that a number of Structural changes take place, especially in the loop and interfacial regions during the course of assembly. The isolated chiller was ``more relaxed'' than the dimer found in the T=3 or T=1 capsids. The isolated dimer does not bind Ca2+ ion and consequently four C-terminal residues are disordered. The FG loop, which interacts with RNA in the Virus, has different conformations in the isolated dimer and the intact Virus Suggesting its flexible nature and the conformational changes that accompany assembly. The isolated choler mutant was much less stable when compared to the assembled capsids, suggesting the importance of inter-subunit interactions and Ca2+ mediated interactions in the stability of the capsids. With this study, SeMV becomes the first icosahedral virus for which X-ray crystal Structures of T=3, T=1 capsids as well as a smaller oligomer of the capsid protein have been determined.

Which One Is Preferred: Myers-Saito Cyclization of Ene-Yne-Allene or Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone? A Theoretical and Experimental Study

A competitive scenario between Myers-Saito (MS) and Garraff-Braverman (GB) cyclization has been created in a molecule. High-level computations indicate a preference for GB over MS cyclization. The activation energies for the rate-determining steps of the GB and MS cyclizations were found to be the same (24.4 kcal/mol) at the B3LYP/6-31G* level of theory; thus, from the kinetic point of view, both reactions are feasible. However, the main biradical intermediate GB2 of the GB reaction is 6.2 kcal/mol lower in energy than the biradical MS2, which is the main intermediate of MS reaction, so GB cyclization is thermodynamically favored over MS cyclization. To verify the prediction by computational techniques, bisenediynyl sulfones 1-4 and bisenediynyl sulfoxide 17 were synthesized. Under basic conditions, these molecules isomerized to a system possessing both the ene-yne-allene and the bisallenic sulfone. The isolation of only one product, identified as the corresponding naphthalene- or benzene-fused sulfone 8-11, indicated the occurrence of GB cyclization as the sole reaction pathway. No product corresponding to the MS cyclization pathway could be isolated. Though the theoretical prediction showed a preference for the GB pathway over the MS pathway, the exclusive preference for GB over MS cyclization is very striking. Further analysis showed that the intramolecular self-quenching nature of the GB pathway may play an important role in the complete preference for this reaction. Apart from the mechanistic studies, these sulfones showed DNA cleavage activity that had an inverse relation with the reactivity order. Our findings are important for the design of artificial DNA-cleaving agents.

Adiabatic quantum computation with a one-dimensional projector Hamiltonian

Adiabatic quantum computation is based on the adiabatic evolution of quantum systems. We analyze a particular class of quantum adiabatic evolutions where either the initial or final Hamiltonian is a one-dimensional projector Hamiltonian on the corresponding ground state. The minimum-energy gap, which governs the time required for a successful evolution, is shown to be proportional to the overlap of the ground states of the initial and final Hamiltonians. We show that such evolutions exhibit a rapid crossover as the ground state changes abruptly near the transition point where the energy gap is minimum. Furthermore, a faster evolution can be obtained by performing a partial adiabatic evolution within a narrow interval around the transition point. These results generalize and quantify earlier works.

Wigner distributions for finite-state systems without redundant phase-point operators

We set up Wigner distributions for N-state quantum systems following a Dirac-inspired approach. In contrast to much of the work in this study, requiring a 2N x 2N phase space, particularly when N is even, our approach is uniformly based on an N x N phase-space grid and thereby avoids the necessity of having to invoke a `quadrupled' phase space and hence the attendant redundance. Both N odd and even cases are analysed in detail and it is found that there are striking differences between the two. While the N odd case permits full implementation of the marginal property, the even case does so only in a restricted sense. This has the consequence that in the even case one is led to several equally good definitions of the Wigner distributions as opposed to the odd case where the choice turns out to be unique.

Evolution of sequence specificity in a restriction endonuclease by a point mutation

Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed with exquisite sequence specificity. REases have originated from the ancestral proteins and evolved new sequence specificities by genetic recombination, gene duplication, replication slippage, and transpositional events. They are also speculated to have evolved from nonspecific endonucleases, attaining a high degree of sequence specificity through point mutations. We describe here an example of generation of exquisitely site-specific REase from a highly-promiscuous one by a single point mutation.

Dynamics after a sweep through a quantum critical point

The coherent quantum evolution of a one-dimensional many-particle system after slowly sweeping the Hamiltonian through a critical point is studied using a generalized quantum Ising model containing both integrable and nonintegrable regimes. It is known from previous work that universal power laws of the sweep rate appear in such quantities as the mean number of excitations created by the sweep. Several other phenomena are found that are not reflected by such averages: there are two different scaling behaviors of the entanglement entropy and a relaxation that is power law in time rather than exponential. The final state of evolution after the quench is not characterized by any effective temperature, and the Loschmidt echo converges algebraically for long times, with cusplike singularities in the integrable case that are dynamically broadened by nonintegrable perturbations.

New insights from a fixed-point analysis of single cell IEEE 802.11 WLANs

We study a fixed-point formalization of the well-known analysis of Bianchi. We provide a significant simplification and generalization of the analysis. In this more general framework, the fixed-point solution and performance measures resulting from it are studied. Uniqueness of the fixed point is established. Simple and general throughput formulas are provided. It is shown that the throughput of any flow will be bounded by the one with the smallest transmission rate. The aggregate throughput is bounded by the reciprocal of the harmonic mean of the transmission rates. In an asymptotic regime with a large number of nodes, explicit formulas for the collision probability, the aggregate attempt rate, and the aggregate throughput are provided. The results from the analysis are compared with ns2 simulations and also with an exact Markov model of the backoff process. It is shown how the saturated network analysis can be used to obtain TCP transfer throughputs in some cases.

Tendency toward crossover of the effective susceptibility exponent from its doubled Ising value to its doubled mean-field value near a double critical point

The critical behavior of osmotic susceptibility in an aqueous electrolyte mixture 1-propanol (1P)+water (W)+potassium chloride is reported. This mixture exhibits re-entrant phase transitions and has a nearly parabolic critical line with its apex representing a double critical point (DCP). The behavior of the susceptibility exponent is deduced from static light-scattering measurements, on approaching the lower critical solution temperatures (TL’s) along different experimental paths (by varying t) in the one-phase region. The light-scattering data analysis substantiates the existence of a nonmonotonic crossover behavior of the susceptibility exponent in this mixture. For the TL far away from the DCP, the effective susceptibility exponent γeff as a function of t displays a nonmonotonic crossover from its single limit three-dimensional (3D)-Ising value ( ∼ 1.24) toward its mean-field value with increase in t. While for that closest to the DCP, γeff displays a sharp, nonmonotonic crossover from its nearly doubled 3D-Ising value toward its nearly doubled mean-field value with increase in t. The renormalized Ising regime extends over a relatively larger t range for the TL closest to the DCP, and a trend toward shrinkage in the renormalized Ising regime is observed as TL shifts away from the DCP. Nevertheless, the crossover to the mean-field limit extends well beyond t>10−2 for the TL’s studied. The observed crossover behavior is attributed to the presence of strong ion-induced clustering in this mixture, as revealed by various structure probing techniques. As far as the critical behavior in complex or associating mixtures with special critical points (like the DCP) is concerned, our results indicate that the influence of the DCP on the critical behavior must be taken into account not only on the renormalization of the critical exponent but also on the range of the Ising regime, which can shrink with decrease in the influence of the DCP and with the extent of structuring in the system. The utility of the field variable tUL in analyzing re-entrant phase transitions is demonstrated. The effective susceptibility exponent as a function of tUL displays a nonmonotonic crossover from its asymptotic 3D-Ising value toward a value slightly lower than its nonasymptotic mean-field value of 1. This behavior in the nonasymptotic, high tUL region is interpreted in terms of the possibility of a nonmonotonic crossover to the mean-field value from lower values, as foreseen earlier in micellar systems.

Neutral-point balancing of neutral-point-clamped three-level inverter with a front end switched rectifier DC source for the full modulationn range

A switched rectifier DC voltage source three-level neutral-point-clamped (NPC) converter topology is proposed here to alleviate the inverter from capacitor voltage balancing in three-level drive systems. The proposed configuration requires only one DC link with a voltage of half of that needed in a conventional NPC inverter. To obtain a rated DC link voltage, the rectifier DC source is alternately connected in parallel to one of the two series capacitors using two switches and two diodes with device voltage ratings of half the total DC bus voltage. The frequency at which the voltage source is switched is independent of the inverter and will not affect its operation since the switched voltage source in this configuration balances the capacitors automatically. The proposed configuration can also be used as a conventional two-level inverter in the lower modulation index range, thereby increasing the reliability of the drivesystem. A space-vector-based PWM scheme is used to verify this proposed topology on a laboratory system.

Folding a Polymer via Two-Point Interaction with an External Folding Agent: Use of H-Bonding and Charge-Transfer Interactions

A polymer containing electron-rich aromatic donors (1,5-dialkoxynaphthalene (DAN)) was coerced into a folded state by an external folding agent that contained an electron-deficient aromatic acceptor (pyromellitic diimide (PM)) unit. The donor-containing polymer was designed to carry a tertiary amine moiety in the linking segment, which served as an H-bonding site for reinforcing the interaction with the acceptor containing folding agent that also bore a carboxylic acid group. The H-bonding interaction of the carboxylic acid and the tertiary amine brings the PDI unit between two adjacent DAN units along the polymer backbone to induce charge-transfer (C-T) interactions, and this in turn causes the polymer chain to form a pleated structure. Evidence for the formation of such a pleated structure was obtained from NMR titration studies and also by monitoring the C-T band in their UV-visible spectra. By varying the length of the segment that links the PDI acceptor to the carboxylic acid group, we showed that the most effective folding agent was the one that had a single carbon spacer, as evident from the highest value of the association constant. Control experiments with propionic acid clearly demonstrated the importance of the additional C-T interactions for venerating the folded structures. Further, solution viscosity measurements in the presence of varying amounts of the folding agent revealed a gradual stiffening of the chain in the case of the PDI carrying carboxylic acid, whereas no such affect was seen in the case of simple propionic acid. These observations were supported by D FT calculations of the interactions of a dimeric model of the polymer with the various folding agents; here too the stability of the complex was seen to be highest in the case of the single carbon spacer.

Note: Dynamic point spread function for single and multiphoton fluorescence microscopy

We propose and demonstrate a dynamic point spread function (PSF) for single and multiphoton fluorescence microscopy. The goal is to generate a PSF whose shape and size can be maneuvered from highly localized to elongated one, thereby allowing shallow-to-depth excitation capability during active imaging. The PSF is obtained by utilizing specially designed spatial filter and dynamically altering the filter parameters. We predict potential applications in nanobioimaging and fluorescence microscopy.

Note: Dynamic point spread function for single and multiphoton fluorescence microscopy

We propose and demonstrate a dynamic point spread function (PSF) for single and multiphoton fluorescence microscopy. The goal is to generate a PSF whose shape and size can be maneuvered from highly localized to elongated one, thereby allowing shallow-to-depth excitation capability during active imaging. The PSF is obtained by utilizing specially designed spatial filter and dynamically altering the filter parameters. We predict potential applications in nanobioimaging and fluorescence microscopy.

Electrical and Dielectric Behaviour at the Critical Point of Binary Liquids: Acetonitrile + Cyclohexane

The electrical capacitance and resistance of the binary liquid mixture cyclohexane + acetonitrile are measured in the one phase and two phase regions at spot frequencies between 5 kHz and 100 kHz. This sample has a very low gravity affected (∼0.6 mK) region. In one phase region the capacitance data show a sharp, ∼0.7% increase above background within 0.5 degrees of Tc whereas the resistance has a smooth increase of ∼1.5% above background in a (T−Tc) range of 4 degrees. Two phase values of capacitance and resistance from the coexisting phases are used to determine the critical parameters Tc (critical temperature), Rc (resistance at Tc) and Cc (capacitance at Tc). A precise knowledge of these parameters reduces the uncertainty on the critical exponent 0 for C and R. The one phase capacitance data fit to an (1 - α) exponent in a limited temperature range of 0.2 degrees. Resistance data strongly support an (1 - α) exponent over the entire 5 degree range.

Appropriate Institutions and Economic Growth - one size fits no-one

Modern-day economics is increasingly biased towards believing that institutions matter for growth, an argument that has been further enforced by the recent economic crisis. There is also a wide consensus on what these growth-promoting institutions should look like, and countries are periodically ranked depending on how their institutional structure compares with the best-practice institutions, mostly in place in the developing world. In this paper, it is argued that ”non-desirable” or “second-best” institutions can be beneficial for fostering investment and thus providing a starting point for sustained growth, and that what matters is the appropriateness of institutions to the economy’s distance to the frontier or current phase of development. Anecdotal evidence from Japan and South-Korea is used as a motivation for studying the subject and a model is presented to describe this phenomenon. In the model, the rigidity or non-rigidity of the institutions is described by entrepreneurial selection. It is assumed that entrepreneurs are the ones taking part in the imitation and innovation of technologies, and that decisions on whether or not their projects are refinanced comes from capitalists. The capitalists in turn have no entrepreneurial skills and act merely as financers of projects. The model has two periods, and two kinds of entrepreneurs: those with high skills and those with low skills. The society’s choice of whether an imitation or innovation – based strategy is chosen is modeled as the trade-off between refinancing a low-skill entrepreneur or investing in the selection of the entrepreneurs resulting in a larger fraction of high-skill entrepreneurs with the ability to innovate but less total investment. Finally, a real-world example from India is presented as an initial attempt to test the theory. The data from the example is not included in this paper. It is noted that the model may be lacking explanatory power due to difficulties in testing the predictions, but that this should not be seen as a reason to disregard the theory – the solution might lie in developing better tools, not better just better theories. The conclusion presented is that institutions do matter. There is no one-size-fits-all-solution when it comes to institutional arrangements in different countries, and developing countries should be given space to develop their own institutional structures that cater to their specific needs.

Conditionally One of 'Us' : A Study of Print Media, Minorities and Positioning Practices

This study deals with how ethnic minorities and immigrants are portrayed in the Finnish print media. The study also asks how media users of various ethnocultural backgrounds make sense of these mediated stories. A more general objective is to elucidate negotiations of belonging and positioning practices in an increasingly complex society. The empirical part of the study is based on content analysis and qualitative close reading of 1,782 articles in five newspapers (Hufvudstadsbladet, Vasabladet, Helsingin Sanomat, Iltalehti and Ilta-Sanomat) during various research periods between 1999 and 2007. Four case studies on print media content are followed up by a focus group study involving 33 newspaper readers of Bosnian, Somalian, Russian, and 'native' Finnish backgrounds. The study draws from different academic and intellectual traditions; mainly media and communication studies, sociology and social psychology. The main theoretical framework employed is positioning theory, as developed by Rom Harré and others. Building on this perspective, situational self-positioning, positioning by others, and media positioning are seen as central practices in the negotiation of belonging. In support of contemporary developments in social sciences, some of these negotiations are seen as occurring in a network type of communicative space. In this space, the media form one of the most powerful institutions in constructing, distributing and legitimising values and ideas of who belongs to 'us', and who does not. The notion of positioning always involves an exclusionary potential. This thesis joins scholars who assert that in order to understand inclusionary and exclusionary mechanisms, the theoretical starting point must be a recognition of a decent and non-humiliating society. When key insights are distilled from the five empirical cases and related to the main theories, one of the major arguments put forward is that the media were first and foremost concerned with a minority actor's rightful or unlawful belonging to the Finnish welfare system. However, in some cases persistent stereotypes concerning some immigrant groups' motivation to work, pay taxes and therefore contribute are so strong that a general idea of individualism is forgotten in favour of racialised and stagnated views. Discussants of immigrant background also claim that the positions provided for minority actors in the media are not easy to identify with; categories are too narrow, journalists are biased, the reporting is simplifying and carries labelling potential. Hence, although the will for the communicative space to be more diverse and inclusive exists — and has also in many cases been articulated in charters, acts and codes — the positioning of ethnic minorities and immigrants differs significantly from the ideal.