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Mountain View, CA, United States

Braun E.,Network Physics
Reports on Progress in Physics | Year: 2015

Biological cells present a paradox, in that they show simultaneous stability and flexibility, allowing them to adapt to new environments and to evolve over time. The emergence of stable cell states depends on genotype-to-phenotype associations, which essentially reflect the organization of gene regulatory modes. The view taken here is that cell-state organization is a dynamical process in which the molecular disorder manifests itself in a macroscopic order. The genome does not determine the ordered cell state; rather, it participates in this process by providing a set of constraints on the spectrum of regulatory modes, analogous to boundary conditions in physical dynamical systems. We have developed an experimental framework, in which cell populations are exposed to unforeseen challenges; novel perturbations they had not encountered before along their evolutionary history. This approach allows an unbiased view of cell dynamics, uncovering the potential of cells to evolve and develop adapted stable states. In the last decade, our experiments have revealed a coherent set of observations within this framework, painting a picture of the living cell that in many ways is not aligned with the conventional one. Of particular importance here, is our finding that adaptation of cell-state organization is essentially an efficient exploratory dynamical process rather than one founded on random mutations. Based on our framework, a set of concepts underlying cell-state organization - exploration evolving by global, non-specific, dynamics of gene activity - is presented here. These concepts have significant consequences for our understanding of the emergence and stabilization of a cell phenotype in diverse biological contexts. Their implications are discussed for three major areas of biological inquiry: evolution, cell differentiation and cancer. There is currently no unified theoretical framework encompassing the emergence of order, a stable state, in the living cell. Hopefully, the integrated picture described here will provide a modest contribution towards a physics theory of the cell. © 2015 IOP Publishing Ltd.

Bolmatov D.,Queen Mary, University of London | Trachenko K.,Queen Mary, University of London | Trachenko K.,Network Physics
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

Calculating liquid energy and heat capacity in general form is an open problem in condensed matter physics. We develop a recent approach to liquids from the solid state by accounting for the contribution of anharmonicity and thermal expansion to liquid energy and heat capacity. We subsequently compare theoretical predictions to the experiments results of five commonly discussed liquids, and find a good agreement with no free fitting parameters. We discuss and compare the proposed theory to previous approaches. © 2011 American Physical Society.

Bolmatov D.,Queen Mary, University of London | Brazhkin V.V.,Russian Academy of Sciences | Trachenko K.,Queen Mary, University of London | Trachenko K.,Network Physics
Nature Communications | Year: 2013

Since their discovery in 1822, supercritical fluids have been of enduring interest and have started to be deployed in many important applications. Theoretical understanding of the supercritical state is lacking and is seen to limit further industrial deployment. Here we study thermodynamic properties of the supercritical state and discover that specific heat shows a crossover between two different regimes, an unexpected result in view of currently perceived homogeneity of supercritical state in terms of physical properties. We subsequently formulate a theory of system thermodynamics above the crossover, and find good agreement between calculated and experimental specific heat with no free-fitting parameters. In this theory, energy and heat capacity are governed by the minimal length of the longitudinal mode in the system only, and do not explicitly depend on system-specific structure and interactions. We derive a power law and analyse supercritical scaling exponents in the system above the Frenkel line. © 2013 Macmillan Publishers Limited. All rights reserved.

Green F.,Network Physics
Physics Education | Year: 2012

The cloud chambers described here are large, made from readily available parts, simple to set up and always work. With no source in the chamber, background radiation can be observed. A large chamber means that a long rod containing a weakly radioactive material can be introduced, increasing the chance of seeing decays. Details of equipment and construction are given. © 2012 IOP Publishing Ltd.

The Agua Amarga coastal aquifer has been the object of a succession of anthropogenic interventions over the last 90 years: (a) the operation of saltworks from 1925 to 1975; (b) the withdrawal, since 2003, of groundwater from the aquifer along the coast line; and (c) the programme of pouring seawater over the salt marsh, carried out since 2009, to recover the piezometric levels and the soil moisture conditions. For a better understanding of how these past and present human activities have affected the natural groundwater regime, and to validate certain hypotheses concerning the interpretation of experimental data on temperature depth profiles and piezometric and salinity changes, a numerical fluid flow and solute transport model was designed and applied to the period 1925-2010, using SEAWAT. This model reproduces, in a qualitative and quantitative way, the flow and transport processes that operated during this time, as well as the behaviour of the seawater wedge. © 2013 Copyright 2013 IAHS Press.

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