The field theoretic derivation of the contact value theorem in planar geometries and its modification by the Casimir effect

The contact value theorem for Coulomb gases in planar or film-like geometries is derived using a Hamiltonian field theoretic representation of the system. The case where the film is enclosed by a material of different dielectric constant to that of the film is shown to contain an additional Casimir-like term which is generated by fluctuations of the electric potential about its mean-field value.Comment: Link between Sine-Gordon and Coulomb gas pressures via subtraction of self interaction terms included. Discussion of results within Debye-Huckel approximation included. Added reference

Survival and ice nucleation activity of bacteria as aerosols in a cloud simulation chamber

The residence time of bacterial cells in the atmosphere is predictable by numerical models. However, estimations of their aerial dispersion as living entities are limited by a lack of information concerning survival rates and behavior in relation to atmospheric water. Here we investigate the viability and ice nucleation (IN) activity of typical atmospheric ice nucleation active bacteria (Pseudomonas syringae and P. fluorescens) when airborne in a cloud simulation chamber (AIDA, Karlsruhe, Germany). Cell suspensions were sprayed into the chamber and aerosol samples were collected by impingement at designated times over a total duration of up to 18 h, and at some occasions after dissipation of a cloud formed by depressurization. Aerosol concentration was monitored simultaneously by online instruments. The cultivability of airborne cells decreased exponentially over time with a half-life time of 250 ±30 min (about 3.5 to 4.5 h). In contrast, IN activity remained unchanged for several hours after aerosolization, demonstrating that IN activity was maintained after cell death. Interestingly, the relative abundance of IN active cells still airborne in the chamber was strongly decreased after cloud formation and dissipation. This illustrates the preferential precipitation of IN active cells by wet processes. Our results indicate that from 10⁶ cells aerosolized from a surface, one would survive the average duration of its atmospheric journey estimated at 3.4 days. Statistically, this corresponds to the emission of 1 cell that achieves dissemination every ~33 min m¯² of cultivated crops fields, a strong source of airborne bacteria. Based on the observed survival rates, depending on wind speed, the trajectory endpoint could be situated several hundreds to thousands of kilometers from the emission source. These results should improve the representation of the aerial dissemination of bacteria in numeric models

ABEMUS: platform specific and data informed detection of somatic SNVs in cfDNA

MOTIVATION: The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single nucleotide variants (SNVs) in circulating cell free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs. RESULTS: We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples. AVAILABILITY: ABEMUS is cross-platform and can be installed as R package. The source code is maintained on Github at http://github.com/cibiobcg/abemus and it is also available at CRAN official R repository. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Steric Effects in Electrolytes: A Modified Poisson-Boltzmann Equation

The adsorption of large ions from solution to a charged surface is investigated theoretically. A generalized Poisson--Boltzmann equation, which takes into account the finite size of the ions is presented. We obtain analytical expressions for the electrostatic potential and ion concentrations at the surface, leading to a modified Grahame equation. At high surface charge densities the ionic concentration saturates to its maximum value. Our results are in agreement with recent experiments.Comment: 4 pages, 2 figure

Infrared and optical polarimetry around the low-mass star-forming region NGC 1333 IRAS 4A

We performed J- and R-band linear polarimetry with the 4.2 m William Herschel Telescope at the Observatorio del Roque de los Muchachos and with the 1.6 m telescope at the Observat\'orio do Pico dos Dias, respectively, to derive the magnetic field geometry of the diffuse molecular cloud surrounding the embedded protostellar system NGC 1333 IRAS 4A. We obtained interstellar polarization data for about two dozen stars. The distribution of polarization position angles has low dispersion and suggests the existence of an ordered magnetic field component at physical scales larger than the protostar. Some of the observed stars present intrinsic polarization and evidence of being young stellar objects. The estimated mean orientation of the interstellar magnetic field as derived from these data is almost perpendicular to the main direction of the magnetic field associated with the dense molecular envelope around IRAS 4A. Since the distribution of the CO emission in NGC 1333 indicates that the diffuse molecular gas has a multi-layered structure, we suggest that the observed polarization position angles are caused by the superposed projection along the line of sight of different magnetic field components.Comment: 37 pages, 9 figures, 5 tables, accepted for publication in A

The `Friction' of Vacuum, and other Fluctuation-Induced Forces

The static Casimir effect describes an attractive force between two conducting plates, due to quantum fluctuations of the electromagnetic (EM) field in the intervening space. {\it Thermal fluctuations} of correlated fluids (such as critical mixtures, super-fluids, liquid crystals, or electrolytes) are also modified by the boundaries, resulting in finite-size corrections at criticality, and additional forces that effect wetting and layering phenomena. Modified fluctuations of the EM field can also account for the `van der Waals' interaction between conducting spheres, and have analogs in the fluctuation--induced interactions between inclusions on a membrane. We employ a path integral formalism to study these phenomena for boundaries of arbitrary shape. This allows us to examine the many unexpected phenomena of the dynamic Casimir effect due to moving boundaries. With the inclusion of quantum fluctuations, the EM vacuum behaves essentially as a complex fluid, and modifies the motion of objects through it. In particular, from the mechanical response function of the EM vacuum, we extract a plethora of interesting results, the most notable being: (i) The effective mass of a plate depends on its shape, and becomes anisotropic. (ii) There is dissipation and damping of the motion, again dependent upon shape and direction of motion, due to emission of photons. (iii) There is a continuous spectrum of resonant cavity modes that can be excited by the motion of the (neutral) boundaries.Comment: RevTex, 2 ps figures included. The presentation is completely revised, and new sections are adde

Effective Interactions and Volume Energies in Charged Colloids: Linear Response Theory

Interparticle interactions in charge-stabilized colloidal suspensions, of arbitrary salt concentration, are described at the level of effective interactions in an equivalent one-component system. Integrating out from the partition function the degrees of freedom of all microions, and assuming linear response to the macroion charges, general expressions are obtained for both an effective electrostatic pair interaction and an associated microion volume energy. For macroions with hard-sphere cores, the effective interaction is of the DLVO screened-Coulomb form, but with a modified screening constant that incorporates excluded volume effects. The volume energy -- a natural consequence of the one-component reduction -- contributes to the total free energy and can significantly influence thermodynamic properties in the limit of low-salt concentration. As illustrations, the osmotic pressure and bulk modulus are computed and compared with recent experimental measurements for deionized suspensions. For macroions of sufficient charge and concentration, it is shown that the counterions can act to soften or destabilize colloidal crystals.Comment: 14 pages, including 3 figure

Effective forces in colloidal mixtures: from depletion attraction to accumulation repulsion

Computer simulations and theory are used to systematically investigate how the effective force between two big colloidal spheres in a sea of small spheres depends on the basic (big-small and small-small) interactions. The latter are modeled as hard-core pair potentials with a Yukawa tail which can be both repulsive or attractive. For a repulsive small-small interaction, the effective force follows the trends as predicted by a mapping onto an effective non-additive hard-core mixture: both a depletion attraction and an accumulation repulsion caused by small spheres adsorbing onto the big ones can be obtained depending on the sign of the big-small interaction. For repulsive big-small interactions, the effect of adding a small-small attraction also follows the trends predicted by the mapping. But a more subtle ``repulsion through attraction'' effect arises when both big-small and small-small attractions occur: upon increasing the strength of the small-small interaction, the effective potential becomes more repulsive. We have further tested several theoretical methods against our computer simulations: The superposition approximation works best for an added big-small repulsion, and breaks down for a strong big-small attraction, while density functional theory is very accurate for any big-small interaction when the small particles are pure hard-spheres. The theoretical methods perform most poorly for small-small attractions.Comment: submitted to PRE; New version includes an important quantitative correction to several of the simulations. The main conclusions remain unchanged thoug