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.     

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.     

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     

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     

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.     

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.     

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’     

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.     

A visual description of the convective flow field around the head of a human

Mean velocity data obtained by PIV (Particle Image Velocimetry) around the head of a real-life size breathing thermal manikin are presented for two cases of ‘no breathing’ and ‘continuous exhalation through nose’. Experiments were conducted in a special chamber which provided stationary convective flows around the seated manikin. Results are limited to the plane of symmetry. The paper aims to describe the physical structure of the turbulent flow field by presenting velocity and vorticity data in color graphics.     

On the lyman problem

This paper attempts to answer Lyman's question (1990) on the non-uniqueness in defining the 3D measure of the boundary vorticity-creation rate. Firstly, a straightforward analysis of the vorticity equation introduces a definition of a general vorticity flux-density tensor and its ‘effective’ part. The approach is strictly based on classical field theory and is independent of the constitutive structure of continuous medium. Secondly, the fundamental question posed by Lyman dealing with the ambiguity of the 3D measure of the boundary vorticity-creation rate for incompressible flow is discussed. It is shown that the original 3D measure (for an incompressible Newtonian fluid defined by Panton 1984), which is reminiscent of an analogy to Fourier's law, is in its character ‘effective’ and plays a crucial role in the prognostic vorticity transport equation. The alternative 3D measure proposed by Lyman includes, on the other hand, a ‘non-effective’ part, which plays a role in the local determination of the ‘effective’ measure as well as in a certain diagnostic integral boundary condition.     

Nanocrystalline silicon thin-film transistors with 50-nm-thick deposited channel layer, 10 cm2V-1s-1 electron mobility and 108 on/off current ratio

Thin-film transistors were made using 50-nm-thick directly deposited nanocrystalline silicon channel layers. The transistors have a coplanar top gate structure. The nanocrystalline silicon was deposited from discharges in silane, hydrogen and silicon tetrafluoride. The transistors combine a high electron field effect mobility of ∼10 cm² V^-1s^-1 with a low ‘off’ current of ∼10^-14 A per μm of channel length and an ‘on’/‘off’ current ratio of ∼10⁸. This result shows that transistors made from directly deposited silicon can combine high mobility with low ‘off’ currents. Received: 28 May 2001 / Accepted: 30 May 2001 / Published online: 30 August 2001     

Extracting science from surveys of our Galaxy

Our knowledge of the Galaxy is being revolutionized by a series of photometric, spectroscopic and astrometric surveys. Already an enormous body of data is available from completed surveys, and data of ever-increasing quality and richness will accrue at least until the end of this decade. To extract science from these surveys, we need a class of models that can give probability density functions in the space of the observables of a survey – we should not attempt to ‘invert’ the data from the space of observables into the physical space of the Galaxy. Currently just one class of model has the required capability, the so-called ‘torus models’. A pilot application of torus models to understand the structure of the Galaxy’s thin and thick discs has already produced two significant results: a major revision of our best estimate of the Sun’s velocity with respect to the local standard of rest, and a successful prediction of the way in which the vertical velocity dispersion in the disc varies with distance from the Galactic plane.     

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.     

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.     

On the discovery of the Greisen-Zatzepin-Kuzmin cut-off

The recent claim of the ‘5 sigma’ observation of the Greisen-Zatzepin-Kuzmin cut-off by the HiRes group based on their nine years data is a significant step towards the eventual solution of one of the most intriguing questions in physics for more than 40 years. Recent results from Pierre Auger Observatory seem to confirm the statement. However, the word ‘significance’ is used in the mentioned paper in a sense which is not quite obvious. In the present paper we argue that this claim is a little premature.     

The dynamics of desorption induced by atomic hydrogen: HD/Cu(111)

Recent observations of a direct reaction between adsorbates and hydrogen atoms incident from the gas phase are interpreted in terms of an Eley-Rideal reaction. A detailed comparison of the experimental data for the HD/Cu(111) system with quantum mechanical model calculations corroborates such an interpretation. The peculiar isotope effect observed can be understood from the different dynamical implications of appropriately rescaled potential energy surfaces. The width of the measured time-of-flight spectrum is explained from the overlapping contributions of the populated vibrational levels. The angular distributions are rationalized by contributions both from ‘indirect’ events, where the incident atoms make several bounces in the surface well prior to reaction, and ‘direct’ reactive events.     

Extremes of nuclear structure

With the advent of medium and large gamma detector arrays, it is now possible to look at nuclear structure at high rotational forces. The role of pairing correlations and their eventual breakdown, along with the shell effects have showed us the interesting physics for nuclei at high spins — superdeformation, shape co-existence, yrast traps, alignments and their dramatic effects on nuclear structure and so on. Nuclear structure studies have recently become even more exciting, due to efforts and possibilities to reach nuclei far off from the stability valley. Coupling of gamma ray arrays with ‘filters’, like neutron wall, charged particle detector array, gamma ray total energy and multiplicity castles, conversion electron spectrometers etc gives a great handle to study nuclei produced online with ‘low’ cross-sections. Recently we studied, nuclei in mass region 80 using an array of 8 germanium detectors in conjunction with the recoil mass analyser, HIRA at the Nuclear Science Centre and, most unexpectedly came across the phenomenon of identical bands, with two quasi-particle difference. The discovery of magnetic rotation is another highlight. Our study of light In nucleus, 107In brought us face to face with the ‘dipole’ bands. I plan to discuss some of these aspects. There is also an immensely important development — that of the ‘radioactive ion beams’. The availability of RIB, will probably very dramatically influence our ‘conventional’ concept of nuclear structure. The exotic shapes of these exotic nuclei and some of their expected properties will also be touched upon.     

Conformal invariance and scalar-tensor theories

A new generalisation of Einstein’s theory is proposed which is invariant under conformal mappings. Two scalar fields are introduced in addition to the metric tensor field, so that two special choices of gauge are available for physical interpretation, the ‘Einstein gauge’ and the ‘atomic gauge’. The theory is not unique but contains two adjustable parameters ζ anda. Witha=1 the theory viewed from the atomic gauge is Brans-Dicke theory (ω=−3/2+ζ/4). Any other choice ofa leads to a creation-field theory. In particular the theory given by the choicea=−3 possesses a cosmological solution satisfying Dirac’s ‘large numbers’ hypothesis.     

Einsteinian gravity from a topological action

The curvature-squared model of gravity, in the affine form proposed by Weyl and Yang, is deduced from a topological action in 4D. More specifically, we start from the Pontrjagin (or Euler) invariant. Using the BRST antifield formalism with a double duality gauge fixing, we obtain a consistent quantization in spaces of double dual curvature as classical instanton type background. However, exact vacuum solutions with double duality properties exhibit a ‘vacuum degeneracy’. By modifying the duality via a scale breaking term, we demonstrate that only Einstein’s equations with an induced cosmological constant emerge for the topology of the macroscopic background. This may have repercussions on the problem of ‘dark energy’ as well as ‘dark matter’ modeled by a torsion induced quintaxion.