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Although accumulation of molecular damage is suggested to be an important molecular mechanism of aging, a quantitative link between the dynamics of damage accumulation and mortality of species has so far remained elusive. To address this question, we examine stability properties of a generic gene regulatory network (GRN) and demonstrate that many characteristics of aging and the associated population mortality rate emerge as inherent properties of the critical dynamics of gene regulation and metabolic levels. Based on the analysis of age-dependent changes in gene-expression and metabolic profiles in Drosophila melanogaster, we explicitly show that the underlying GRNs are nearly critical and inherently unstable. This instability manifests itself as aging in the form of distortion of gene expression and metabolic profiles with age, and causes the characteristic increase in mortality rate with age as described by a form of the Gompertz law. In addition, we explain late-life mortality deceleration observed at very late ages for large populations. We show that aging contains a stochastic component, related to accumulation of regulatory errors in transcription/translation/metabolic pathways due to imperfection of signaling cascades in the network and of responses to environmental factors. We also establish that there is a strong deterministic component, suggesting genetic control. Since mortality in humans, where it is characterized best, is strongly associated with the incidence of age-related diseases, our findings support the idea that aging is the driving force behind the development of chronic human diseases., Comment: 22 pages, 9 figures

We apply a phenomenological theory of polar liquids to calculate the interaction energy between two plane surfaces at nm-distances. We show that depending on the properties of the surface-liquid interfaces, the interacting surfaces induce polarization of the liquid in different ways. We find, in full agreement with available experiments, that if the interfaces are mostly hydrophobic, then the interaction is attractive and relatively long-ranged (interaction decay length \lambda\sim1.2\, nm). The water molecules are net polarized parallel to the surfaces in this case. If the surfaces are mostly hydrophilic, then the molecules are polarized against the surfaces, and the interaction becomes repulsive, but at a short-range (\lambda\sim0.2\, nm). Finally, we predict there exists an intermediate regime, where the surfaces fail to order the water molecules, the interaction becomes much weaker, attractive and, at relatively small distances, decays with the inverse square of the distance between the surfaces., Comment: 4 pages, 2 png figures

We investigate the nature of the phase transition occurring in a planar XY-model spin system with dipole-dipole interactions. It is demonstrated that a Berezinskii-Kosterlitz-Thouless (BKT) type of phase transition always takes place at a finite temperature separating the ordered (ferro) and the disordered (para) phases. The low-temperature phase corresponds to an ordered state with thermal fluctuations, composed of a "gas" of bound vortex-antivortex pairs, which would, when considered isolated, be characterized by a constant vortex-antivortex attraction force which is due to the dipolar interaction term in the Hamiltonian. Using a topological charge model, we show that small bound pairs are easily polarized, and screen the vortex-antivortex interaction in sufficiently large pairs. Screening changes the linear attraction potential of vortices to a logarithmic one, and leads to the familiar pair dissociation mechanism of the BKT type phase transition. The topological charge model is confirmed by numerical simulations, in which we demonstrate that the transition temperature slightly increases when compared with the BKT result for short-range interactions., Comment: 9 pages of RevTex4-1, 4 figures

We analyze thermodynamics of water samples confined in nanopores and prove that although the freezing temperature can be dramatically lower, the suppression of the ice nucleation leading to the freezing temperature depression is a truly macroscopic effect rather than a consequence of microscopic interactions. The freezing transition itself is a truly collective phenomenon described by a macroscopic order parameter (the nearly homogeneous density of the liquid within the pore away from the pores wall) exactly in the same way as in the bulk liquid. The thermodynamics properties of the confined and the bulk liquid can be described by macroscopic thermodynamics and be readily related to each other simply by proper inclusion of the additional Laplace pressure exerted by the solid-liquid boundary., Comment: 3 pages, 1 eps figure

We studied dielectric properties of nano-sized liquid water samples confined in polymerized silicates MCM-41 characterized by the porous sizes \sim 3-10nm. We report the direct measurements of the dielectric constant by the dielectric spectroscopy method at frequencies 25Hz-1MHz and demonstrate clear signatures of the second-order phase transition of ferroelectric nature at temperatures next to the \lambda- point in the bulk supercooled water. The presented results support the previously developed polar liquid phenomenology and hence establish its applicability to model actual phenomena in liquid water., Comment: 4 pages, single figure

We analyze deficiencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of biomolecules with charged groups. The procedure is only a few percents wrong for molecular configurations of arbitrary sizes, provides explicit values for the reaction field potential at any point of the molecular interior, water polarization at the surface of the molecule, both the solvation energy value and its derivatives suitable for Molecular Dynamics (MD) simulations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as solvation energies contributions to a molecular complex formation., Comment: multiple changes, improved text, material and refs added

We apply recently developed phenomenological theory of polar liquids to calculate the repulsive pressure between two hydrophilic membranes at nm-distances. We find that the repulsion does show up in the model and the solution to the problem fits the published experimental data well both qualitatively and quantitatively. Moreover, we find that the repulsion is practically independent on temperature, and thus put some extra weight in favour of the so called hydration over entropic hypothesis for the membranes interactions explanation. The calculation is a good proof of concept example a continuous water model application to non-trivial interactions on -size bodies in water arising from long-range correlations between the water molecules., Comment: 4 pages, 1 png figure, massive update

We develop a series of approximations to calculate free energy of a polar liquid. We show that long range nature of dipole interactions between the molecules leads to para-electric state instability at low temperatures and to a second-order phase transition. We establish the transition temperature, T_{c}, both within mean field and ring diagrams approximation and show that the ferro-electric transition may play an important role explaining a number of peculiar properties of supercooled water, such as weak singularity of dielectric constant as well as to a large extent anomalous density behavior. Finally we discuss the role of fluctuations, shorter range forces and establish connections with phenomenological models of polar liquids., Comment: 5 pages, 1 eps figure, density anomaly at T=4C analysis added