Domain Growth, Wetting and Scaling in Porous Media

The lattice Boltzmann (LB) method is used to study the kinetics of domain growth of a binary fluid in a number of geometries modeling porous media. Unlike the traditional methods which solve the Cahn-Hilliard equation, the LB method correctly simulates fluid properties, phase segregation, interface dynamics and wetting. Our results, based on lattice sizes of up to $4096\times 4096$, do not show evidence to indicate the breakdown of late stage dynamical scaling, and suggest that confinement of the fluid is the key to the slow kinetics observed. Randomness of the pore structure appears unnecessary.Comment: 13 pages, latex, submitted to PR

Geodesics of electrically and magnetically charged test particles in the Reissner-Nordstr\"om space-time: analytical solutions

We present the full set of analytical solutions of the geodesic equations of charged test particles in the Reissner-Nordstr\"om space-time in terms of the Weierstra{\ss} $\wp$, $\sigma$ and $\zeta$ elliptic functions. Based on the study of the polynomials in the $\vartheta$ and $r$ equations we characterize the motion of test particles and discuss their properties. The motion of charged test particles in the Reissner-Nordstr\"om space-time is compared with the motion of neutral test particles in the field of a gravitomagnetic monopole. Electrically or magnetically charged particles in the Reissner-Nordstr\"om space-time with magnetic or electric charges, respectively, move on cones similar to neutral test particles in the Taub-NUT space-times

Epigenetic and phenotypic variability in populaitons of Schistosoma mansoni - a possible kick-off for adaptative host/parasite evolution

International audienceEpigenetics, the science of heritable but modifiable information, is now a well-accepted component of many research fields. Nevertheless, epigenetics has not yet found broad appreciation in one of the most exciting fields of biology: the comprehension of evolution. This is surprising, since the reason for the existence of this alternative information-transmitting system lies certainly in the evolutionary advantage it provides. Theoretical considerations support a model in which epigenetic mechanisms allow for increasing phenotypic variability and permit populations to explore the adaptive landscape without modifications of the genotype. The data presented here support the view that modulating the epigenotype of the human bloodfluke Schistosoma mansoni by treatment of larvae with histone deacetylase inhibitor leads indeed to an increase of phenotypic variability. It is therefore conceivable that environmentally induced changes in the epigenotype release new phenotypes on which selection can act and that this process is the first step in adaptive evolution

Is there life inside black holes?

Bound inside rotating or charged black holes, there are stable periodic planetary orbits, which neither come out nor terminate at the central singularity. Stable periodic orbits inside black holes exist even for photons. These bound orbits may be defined as orbits of the third kind, following the Chandrasekhar classification of particle orbits in the black hole gravitational field. The existence domain for the third kind orbits is rather spacious, and thus there is place for life inside supermassive black holes in the galactic nuclei. Interiors of the supermassive black holes may be inhabited by civilizations, being invisible from the outside. In principle, one can get information from the interiors of black holes by observing their white hole counterparts.Comment: 11 pages, 5 figures; references adde

Museum epigenomics: Characterizing cytosine methylation in historic museum specimens

Museum genomics has transformed the field of collections‐based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well preserved ancient tissues. This approach has not yet been tested in traditionally prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we developed and tested methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulphite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013–2016. We successfully estimated methylation in specimens of all age groups, although older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1–3 years old), which may reflect post‐mortem hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, studies will need to accommodate the large variance in the quantity of data produced by older specimens.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/162784/5/men13115.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162784/4/men13115-sup-0003-AppendixS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162784/3/men13115-sup-0001-FigS1-S2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162784/2/men13115_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162784/1/men13115-sup-0002-TableS1-S2.pd

Hydrodynamic Spinodal Decomposition: Growth Kinetics and Scaling Functions

We examine the effects of hydrodynamics on the late stage kinetics in spinodal decomposition. From computer simulations of a lattice Boltzmann scheme we observe, for critical quenches, that single phase domains grow asymptotically like $t^{\alpha}$, with $\alpha \approx .66$ in two dimensions and $\alpha \approx 1.0$ in three dimensions, both in excellent agreement with theoretical predictions.Comment: 12 pages, latex, Physical Review B Rapid Communication (in press

A Lattice Boltzmann method for simulations of liquid-vapor thermal flows

We present a novel lattice Boltzmann method that has a capability of simulating thermodynamic multiphase flows. This approach is fully thermodynamically consistent at the macroscopic level. Using this new method, a liquid-vapor boiling process, including liquid-vapor formation and coalescence together with a full coupling of temperature, is simulated for the first time.Comment: one gzipped tar file, 19 pages, 4 figure

Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies

Bisulfite treatment can be used to ascertain the methylation states of individual cytosines in DNA. Ideally, bisulfite treatment deaminates unmethylated cytosines to uracils, and leaves 5-methylcytosines unchanged. Two types of bisulfite-conversion error occur: inappropriate conversion of 5-methylcytosine to thymine, and failure to convert unmethylated cytosine to uracil. Conventional bisulfite treatment requires hours of exposure to low-molarity, low-temperature bisulfite (‘LowMT’) and, sometimes, thermal denaturation. An alternate, high-molarity, high-temperature (‘HighMT’) protocol has been reported to accelerate conversion and to reduce inappropriate conversion. We used molecular encoding to obtain validated, individual-molecule data on failed- and inappropriate-conversion frequencies for LowMT and HighMT treatments of both single-stranded and hairpin-linked oligonucleotides. After accounting for bisulfite-independent error, we found that: (i) inappropriate-conversion events accrue predominantly on molecules exposed to bisulfite after they have attained complete or near-complete conversion; (ii) the HighMT treatment is preferable because it yields greater homogeneity among sites and among molecules in conversion rates, and thus yields more reliable data; (iii) different durations of bisulfite treatment will yield data appropriate to address different experimental questions; and (iv) conversion errors can be used to assess the validity of methylation data collected without the benefit of molecular encoding

Epigenetics as a mechanism driving polygenic clinical drug resistance

Aberrant methylation of CpG islands located at or near gene promoters is associated with inactivation of gene expression during tumour development. It is increasingly recognised that such epimutations may occur at a much higher frequency than gene mutation and therefore have a greater impact on selection of subpopulations of cells during tumour progression or acquisition of resistance to anticancer drugs. Although laboratory-based models of acquired resistance to anticancer agents tend to focus on specific genes or biochemical pathways, such 'one gene : one outcome' models may be an oversimplification of acquired resistance to treatment of cancer patients. Instead, clinical drug resistance may be due to changes in expression of a large number of genes that have a cumulative impact on chemosensitivity. Aberrant CpG island methylation of multiple genes occurring in a nonrandom manner during tumour development and during the acquisition of drug resistance provides a mechanism whereby expression of multiple genes could be affected simultaneously resulting in polygenic clinical drug resistance. If simultaneous epigenetic regulation of multiple genes is indeed a major driving force behind acquired resistance of patients' tumour to anticancer agents, this has important implications for biomarker studies of clinical outcome following chemotherapy and for clinical approaches designed to circumvent or modulate drug resistance

Coupled Motions Direct Electrons along Human Microsomal P450 Chains

Directional electron transfer through biological redox chains can be achieved by coupling reaction chemistry to conformational changes in individual redox enzymes