Emerging molecular diversity from the intra-molecular Ugi reaction: iterative efficiency in medicinal chemistry

This review details a now established area within the isonitrile multi-component reaction (IMCR) field of study, namely employing bi-functional reagents in the Ugi reaction for the construction of screening sets with the additional element or even possibly ‘metric’ of enhanced ‘iterative efficiency potential’ The concept of ‘iterative efficiency’ will be briefly introduced, coupled with discussion on new synthetic routes to select bi-functional IMCR precursors and their use in the generation of pharmacologically relevant ‘molecular diversity’     

Schrödinger’s Cat Meets Einstein’s Twins: A Superposition of Different Clock Times

The phenomenon of quantum superposition, which allows a physical system to exist in different states ‘simultaneously’, is one of the most bizarre notions in physics. Here we illustrate an even more bizarre example of it: a superposed state of a physical system consisting of both an ‘older’ version and a ‘younger’ version of that system. This can be accomplished by exploiting the special relativistic effect of time dilation featuring in Einstein’s famous twin paradox.     

Analysis of protein folds using protein contact networks

Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out the biophysical and biochemical functions. Proteins are defined as having a common ‘fold’ if they have major secondary structural elements with same topological connections. It is known that folding mechanisms are largely determined by a protein’s topology rather than its interatomic interactions. The native state protein structures can, thus, be modelled, using a graph-theoretical approach, as coarse-grained networks of amino acid residues as ‘nodes’ and the inter-residue interactions/contacts as ‘links’. Using the network representation of protein structures and their 2D contact maps, we have identified the conserved contact patterns (groups of contacts) representing two typical folds — the EF-hand and the ubiquitin-like folds. Our results suggest that this direct and computationally simple methodology can be used to infer about the presence of specific folds from the protein’s contact map alone.      

Maxwell’s demon and the second law of thermodynamics

An idealized, two-dimensional Maxwell demon is described which incorporates an irreversible process. The vertex of the device acts as a purely mechanical ‘trap door’. This idealized mechanism is found to generate a violation of the second law of thermodynamics. These results indicate that the second law of thermodynamics is not valid in general for idealized, irreversible systems.     

What is Erased in the Quantum Erasure?

In this paper, we re-examine a series of gedanken welcher Weg (WW) experiments introduced by Scully, Englert and Walther that contain the essential ideas underlying the quantum eraser. For this purpose we use the Bohm model which gives a sharp picture of the behaviour of the atoms involved in these experiments. This model supports the thesis that interference disappears in such WW experiments, even though the centre of mass wave function remains coherent throughout the experiment. It also shows exactly what it means to say ‘that the interference can be restored by manipulating the WW detectors long after the atoms have passed’. It does not support Wheeler’s notion that ‘the past is undefined and undefinable without the observation (in the present)’.     

All basic condensed matter physics phenomena and notions mirror in biology — A hypothesis,two examples and a novel prediction

A few billion years of evolutionary time and the complex process of ‘selection’ has given biology an opportunity to explore a variety of condensed matter phenomena and situations, some of which have been discovered by humans in the laboratory, that too only in extreme non-biological conditions such as low temperatures, high purity, high pressure etc., in the last centuries. Biology, at some level, is a complex and self-regulated condensed matter system compared to the ‘inanimate’ condensed matter systems such as liquid ⁴He, liquid water or a piece of graphite. In this article I propose a hypothesis that ‘all basic condensed matter physics phenomena and notions (already known and ones yet to be discovered) mirror in biology’. I explain this hypothesis by considering the idea of ‘Bose condensation’ or ‘momentum space order’ and discuss two known example of quantum magnetism encountered in biology. I also provide some new and rather speculative possibility, from light harvesting in biological photosynthesis, of mesoscopic excition condensation related phenomena at room temperature.     

How To Play Two-Player Restricted Quantum Games with 10 Cards

We show that it is possible to play ‘restricted’ two-player quantum games proposed originally by Marinatto and Weber (Phys. Lett. A 272:291–303, 2000) by purely macroscopic means, in the simplest case having as the only equipment a pack of 10 cards. Our example shows also that some apparently ‘genuine quantum’ results, even those that emerge as a consequence of dealing with entangled states, can be obtained by suitable application of Kolmogorovian probability calculus and secondary-school mathematics, without application of the ‘Hilbert space machinery’.     

Against ‘Realism’

We examine the prevalent use of the phrase “local realism” in the context of Bell’s Theorem and associated experiments, with a focus on the question: what exactly is the ‘realism’ in ‘local realism’ supposed to mean? Carefully surveying several possible meanings, we argue that all of them are flawed in one way or another as attempts to point out a second premise (in addition to locality) on which the Bell inequalities rest, and (hence) which might be rejected in the face of empirical data violating the inequalities. We thus suggest that the phrase ‘local realism’ should be banned from future discussions of these issues, and urge physicists to revisit the foundational questions behind Bell’s Theorem.     

Wigner distributions for finite dimensional quantum systems: An algebraic approach

We discuss questions pertaining to the definition of ‘momentum’, ‘momentum space’, ‘phase space’ and ‘Wigner distributions’; for finite dimensional quantum systems. For such systems, where traditional concepts of ‘momenta’ established for continuum situations offer little help, we propose a physically reasonable and mathematically tangible definition and use it for the purpose of setting up Wigner distributions in a purely algebraic manner. It is found that the point of view adopted here is limited to odd dimensional systems only. The mathematical reasons which force this situation are examined in detail     

Effect of different types of pseudopotentials on study of electronic dispersion for graphene and a (5,5) SWCNT

We study the electronic dispersion for a graphene sheet and also a (5,5) single wall carbon nanotube (SWCNT) by using the PWscf code from the ‘Quantum Espresso’ package. Two different types of pseudopotentials, ‘norm conserving’ and ‘ultra soft’, have been employed and the results are more or less similar up to the Fermi level. By energy relaxation, it was found that, if the inter-layer distance of graphite expands up to 4.5 times its in-layer (hexagonal) lattice constant, then each layer can be considered as an individual graphene sheet and, in a bundle of (5,5) SWCNTs, the optimum separation between the tubes’ centers is about 19 a.u. and, if it expands to 22 a.u., then a single wall tube consideration can be made. The calculated band structure and density of states (DOS) for the (5,5) SWCNT show that in the vicinity of the Fermi level there is no energy gap (so that it is metallic) and there is a general agreement between them and zone-folding studies or other ab initio methods in the literature. The effects of curvature on the band shifts and DOS have been considered, and they magnify the departure from Mintmire and White’s universal prediction. PACS  71.20.Tx; 71.15.Mb; 73.61.Wp     

Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers

Summary The data for 3.8 million compounds from structural databases of 32 providers were gathered and stored in a single chemical database. Duplicates are removed using the IUPAC International Chemical Identifier. After this, 2.6 million compounds remain. Each database and the final one were studied in term of uniqueness, diversity, frameworks, ‘drug-like’ and ‘lead–like’ properties. This study also shows that there are more than 87 000 frameworks in the database. It contains 2.1 million ‘drug-like’ molecules among which, more than one million are ‘lead-like’. This study has been carried out using ‘ScreeningAssistant’, a software dedicated to chemical databases management and screening sets generation. Compounds are stored in a MySQL database and all the operations on this database are carried out by Java code. The druglikeness and leadlikeness are estimated with ‘in–house’ scores using functions to estimate convenience to properties; unicity using the InChI code and diversity using molecular frameworks and fingerprints. The software has been conceived in order to facilitate the update of the database. ‘ScreeningAssistant’ is freely available under the GPL license.     

Temperature dependence of the sensitivity of a long-range surface plasmon optical sensor

The temperature dependence of the sensitivity of an optical sensor based on long-range surface plasmon resonance (LRSPR) is studied via theoretical modeling. Both the ‘angular interrogation’ and the ‘wavelength interrogation’ modes of operation are studied. In addition, the variation of the full width at half maximum of the LRSPR ‘reflectance dip’ is also studied as a function of temperature, which ultimately determines the temperature dependence of the sensitivity of the sensor when the reflectance is monitored at a fixed incident angle (‘reflectance interrogation’). It is found that while most of the time only the ‘reflectance interrogation’ mode leads to improved sensitivity for the LRSPR sensor compared to a conventional SPR sensor, the temperature stability of the operation of the LRSPR sensor is generally higher than (or at least comparable to) that of the SPR sensor. PACS 73.20.Mf; 07.07.Df     

Division Algebras and Quantum Theory

Quantum theory may be formulated using Hilbert spaces over any of the three associative normed division algebras: the real numbers, the complex numbers and the quaternions. Indeed, these three choices appear naturally in a number of axiomatic approaches. However, there are internal problems with real or quaternionic quantum theory. Here we argue that these problems can be resolved if we treat real, complex and quaternionic quantum theory as part of a unified structure. Dyson called this structure the ‘three-fold way’. It is perhaps easiest to see it in the study of irreducible unitary representations of groups on complex Hilbert spaces. These representations come in three kinds: those that are not isomorphic to their own dual (the truly ‘complex’ representations), those that are self-dual thanks to a symmetric bilinear pairing (which are ‘real’, in that they are the complexifications of representations on real Hilbert spaces), and those that are self-dual thanks to an antisymmetric bilinear pairing (which are ‘quaternionic’, in that they are the underlying complex representations of representations on quaternionic Hilbert spaces). This three-fold classification sheds light on the physics of time reversal symmetry, and it already plays an important role in particle physics. More generally, Hilbert spaces of any one of the three kinds—real, complex and quaternionic—can be seen as Hilbert spaces of the other kinds, equipped with extra structure.     

Strong pionic intermittency in ‘cold’ events in12C-AgBr interactions at 4.5 A GeV

In this paper intermittent behaviour of the pions from ‘cold’ and ‘hot’ classes of events from¹²C-AgBr interactions at 4.5 A GeV has been studied, separately. The results reveal strong intermittent pattern in case of ‘cold’ class of events.     

Top-gathering pillar array of hybrid organic–inorganic material by means of self-organization

Two-dimensional (2D) pillar arrays with submicrometer to micrometer repetitions have been fabricated from hybrid organic–inorganic material by mask lithography or multi-beam interference lithography. The type of array structure depends on structural parameters such as the pillar height, diameter and distance between neighboring pillars. Two kinds of periodic arrays, 2D arrays and ‘top-gathering’ arrays, can be obtained by controlling the structural parameters. In the top-gathering arrays, the pillars are gathered at the top by means of self-organization, and ‘top-gathering’ units composed of four pillars can be formed. PACS 68.35.Gy; 81.20.Fw; 82.50.-m     

Studies of polarization/self-depolarization and electret-type effect in AgI

A novel d.c. polarization/self-depolarization study and electret-type effect in AgI are reported. AgI pellets of varying thicknesses, placed between two blocking (graphite) electrodes, were subjected to an external d.c. potential. A state of complete polarization was attained within ∼10 min, irrespective of the sample thickness. At this state, the potential difference, developed across the sample pellet as a result of polarization/accumulation of mobile Ag⁺ ions at the bulk/negative electrode interface, was measured experimentally. The potential difference, obtained immediately after the removal of the external d.c. source, has been referred to as ‘instant peak potential (V_p)’. As soon as the external voltage source is switched off, a process of self-depolarization is initiated due to the chemical/self diffusion of polarized mobile Ag⁺ ions throughout the bulk. ‘V_p’ gives a direct information regarding the extent of mobile ion concentration (n). ‘V_p’ measurements were carried out as a function of temperature and ‘Log V_p vs 1/T’ variation was compared with the ‘Log n vs 1/T’ Arrhenius plot, reported earlier in an entirely independent study. The two variations are almost analogous. This, in turn, supported as an earlier assertion that the abrupt conductivity increase in α-AgI, after β→α-phase transition at ∼147 °C, is predominantly due to the excessive increase in ‘n’. Furthermore, it has also been revealed that the Ag⁺ ions play another unique role which led to the existence of ‘persistent polarization’ states in AgI. These states are identical to the ‘electret-type effects’, observed in a number of dielectric materials. The polarization state persisted for very long time in ‘thermally stimulated polarized’ sample. A detailed investigation of the persistence/retention of polarization in the thermally-stimulated-polarized sample is reported.     

An invitation to higher gauge theory

In this easy introduction to higher gauge theory, we describe parallel transport for particles and strings in terms of 2-connections on 2-bundles. Just as ordinary gauge theory involves a gauge group, this generalization involves a gauge ‘2-group’. We focus on 6 examples. First, every abelian Lie group gives a Lie 2-group; the case of U(1) yields the theory of U(1) gerbes, which play an important role in string theory and multisymplectic geometry. Second, every group representation gives a Lie 2-group; the representation of the Lorentz group on 4d Minkowski spacetime gives the Poincaré 2-group, which leads to a spin foam model for Minkowski spacetime. Third, taking the adjoint representation of any Lie group on its own Lie algebra gives a ‘tangent 2-group’, which serves as a gauge 2-group in 4d BF theory, which has topological gravity as a special case. Fourth, every Lie group has an ‘inner automorphism 2-group’, which serves as the gauge group in 4d BF theory with cosmological constant term. Fifth, every Lie group has an ‘automorphism 2-group’, which plays an important role in the theory of nonabelian gerbes. And sixth, every compact simple Lie group gives a ‘string 2-group’. We also touch upon higher structures such as the ‘gravity 3-group’, and the Lie 3-superalgebra that governs 11-dimensional supergravity.     

Some Remarks on the Notion of Separability Within the Creation Discovery View

In this paper we present Aerts’ vessels of water model which violates Bell inequalities, and discuss how this fits in the Creation Discovery View in the context of the Operational Quantum Logic approach. We analyze the 2 different ways in which correlation is classically observed, either as pre-existing ‘independent of measurement’ or established by sending a signal, hence limited by the speed of light. As the Aerts’ model shows, there is yet a third possibility, namely a situation in which correlation is potentially present, but only actualized to its full extent by the act of measurement. This creation-discovery view can be applied to the quantum mechanical situation of two entangled photons, and shows that in the debate of understanding ‘what is really going on in Aspects experiments’ an alternative explanation can be found, in which potentiality, creation and discovery play a central role.     

Observability of the effects of curl-free magnetic vector potential on the macroscale and the nature of the ‘transition amplitude wave’

We discuss here the prediction, based on a formalism by the author, on the observable effects of a curl-free magnetic vector potential on the macroscale as against the microscale of the Aharonov-Bohm effect. A new quantum concept — the ‘transition amplitude wave’ — postulated in the formalism has already been shown to exhibit matter wave manifestations in the form of one-dimensional interference effects on the macroscale. It was predicted by the formalism that the same entity would lead to the detection of a curl-free magnetic vector potential on the macroscale. We describe here the manner of generation of this quantum entity in an inelastic scattering episode and work out an algorithm to observe this radically new phenomenon, the detection of a curl-free magnetic vector potential on the macroscale. We determine the various characteristic features of such an observation which can then be looked for experimentally so as to verify the predicted effect, establishing thereby the physical reality of the new quantum entity, and to fully validate the formalism predicting it. It is also shown that this ‘transition amplitude wave’ can be regarded as a novel kind of ‘quasiparticle’ excited in the charged particle trajectory as a consequence of the scattering episode.