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.     

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.     

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.     

Mass formulae for Λ-hypernuclei

Simple considerations regarding the Hamiltonian and the ground state wavefunctions of Λ-hypernuclei are used to derive several mass formulae. The parameters that occur in the mass formulae are determined by fitting the experimental binding energies. Information regarding the various interactions in hypernuclal is deduced from the values of these parameters. The ‘best’ mass formula is further used to predict energies of other light hypernuclei. Relationship between binding energies are also suggested and checked with observed data.     

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.     

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     

The case for the cosmological constant

I present a short overview of current observational results and theoretical models for a cosmological constant. The main motivation for invoking a small cosmological constant (or A-term) at the present epoch has to do with observations of high redshift Type Ia supernovae which suggest an accelerating universe. A flat accelerating universe is strongly favoured by combining supernovae observations with observations of CMB anisotropies on degree scales which give the ‘best-fit’ values Θ_A ⋍ 0.7 and Θ _m ⋍ 0.3. A time dependent cosmological A-term can be generated by scalar field models with exponential and power law potentials. Some of these models can alleviate the ‘fine tuning’ problem which faces the cosmological constant.     

Factorised steady states and condensation transitions in nonequilibrium systems

Systems driven out of equilibrium can often exhibit behaviour not seen in systems in thermal equilibrium —for example phase transitions in one-dimensional systems. In this talk I will review a simple model of a nonequilibrium system known as the ‘zero-range process’ and its recent developments. The nonequilibrium stationary state of this model factorises and this property allows a detailed analysis of several ‘condensation’ transitions wherein a finite fraction of the constituent particles condenses onto a single lattice site. I will then consider a more general class of mass transport models, encompassing continuous mass variables and discrete time updating, and present a necessary and sufficient condition for the steady state to factorise. The property of factorisation again allows an analysis of the condensation transitions which may occur.     

Low-coherence interferometry by intensity correlation

‘Low-coherence interferometry’ is an old technique which has had a wide development recently, and is based on the fact that interference with a path difference much longer that the coherence length gives rise to a ‘channeled spectrum’, which can be detected either by a dispersive spectroscope or by a second interferometer with a variable delay. We have tested an alternative way to detect path differences in this kind of interferometry, by analyzing the output intensity fluctuation correlations by a radiofrequency spectrum analyzer, and Fourier transforming the data. This method is suitable for very long path differences. The experiments have been performed with different lengths of single-mode fibre, in Mach–Zehnder and Fabry–Pérot configurations. Received: 30 March 2000 / Revised version: 17 Juli 2000 / Published online: 20 September 2000     

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.     

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.      

Neutrino anomalies without oscillations

I review explanations for the three neutrino anomalies (solar, atmospheric and LSND) which go beyond the ‘conventional’ neutrino oscillations induced by mass-mixing. Several of these require non-zero neutrino masses as well.     

Optico-Mechanical Analogy: an Axiomatic Approach

An axiomatic characterization of a ‘two-level Hamiltonian structure’ is proposed, which expresses the optico-mechanical analogy by representing optics and mechanics as (disjoint) classes of models satisfying the axioms. There is the ‘Hamilton–Jacobi level’, which involves a differential manifold on which the characteristic function satisfying the Hamilton–Jacobi equation is defined; and the ‘symplectic level’, involving the Hamiltonian, defined on the cotangent bundle of the manifold. The two levels, with the (analogous) structures on them, concern both optics and mechanics.     

Lowx physics and structure functions

In this talk I review the behaviour of structure functions at low values of Bjorkenx and discuss the theoretical underpinnings with particular attention to resummation schemes. I present the need for ‘less inclusive’ events to distinguish between various resummation schemes and discuss the various difficulties in differentiating experimentally between different schemes.     

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.     

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.     

The Possibilist Transactional Interpretation and Relativity

A recent ontological variant of Cramer’s Transactional Interpretation, called “Possibilist Transactional Interpretation” or PTI, is extended to the relativistic domain. The present interpretation clarifies the concept of ‘absorption,’ which plays a crucial role in TI (and in PTI). In particular, in the relativistic domain, coupling amplitudes between fields are interpreted as amplitudes for the generation of confirmation waves (CW) by a potential absorber in response to offer waves (OW), whereas in the nonrelativistic context CW are taken as generated with certainty. It is pointed out that solving the measurement problem requires venturing into the relativistic domain in which emissions and absorptions take place; nonrelativistic quantum mechanics only applies to quanta considered as ‘already in existence’ (i.e., ‘free quanta’), and therefore cannot fully account for the phenomenon of measurement, in which quanta are tied to sources and sinks.