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

Lattice Boltzmann Simulation of Non-Ideal Fluids

A lattice Boltzmann scheme able to model the hydrodynamics of phase separation and two-phase flow is described. Thermodynamic consistency is ensured by introducing a non-ideal pressure tensor directly into the collision operator. We also show how an external chemical potential can be used to supplement standard boundary conditions in order to investigate the effect of wetting on phase separation and fluid flow in confined geometries. The approach has the additional advantage of reducing many of the unphysical discretisation problems common to previous lattice Boltzmann methods.Comment: 11 pages, revtex, 4 Postscript figures, uuencode

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

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

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

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

The Surgical Infection Society revised guidelines on the management of intra-abdominal infection

Background: Previous evidence-based guidelines on the management of intra-abdominal infection (IAI) were published by the Surgical Infection Society (SIS) in 1992, 2002, and 2010. At the time the most recent guideline was released, the plan was to update the guideline every five years to ensure the timeliness and appropriateness of the recommendations. Methods: Based on the previous guidelines, the task force outlined a number of topics related to the treatment of patients with IAI and then developed key questions on these various topics. All questions were approached using general and specific literature searches, focusing on articles and other information published since 2008. These publications and additional materials published before 2008 were reviewed by the task force as a whole or by individual subgroups as to relevance to individual questions. Recommendations were developed by a process of iterative consensus, with all task force members voting to accept or reject each recommendation. Grading was based on the GRADE (Grades of Recommendation Assessment, Development, and Evaluation) system; the quality of the evidence was graded as high, moderate, or weak, and the strength of the recommendation was graded as strong or weak. Review of the document was performed by members of the SIS who were not on the task force. After responses were made to all critiques, the document was approved as an official guideline of the SIS by the Executive Council. Results: This guideline summarizes the current recommendations developed by the task force on the treatment of patients who have IAI. Evidence-based recommendations have been made regarding risk assessment in individual patients; source control; the timing, selection, and duration of antimicrobial therapy; and suggested approaches to patients who fail initial therapy. Additional recommendations related to the treatment of pediatric patients with IAI have been included. Summary: The current recommendations of the SIS regarding the treatment of patients with IAI are provided in this guideline

Transgene Expression Is Associated with Copy Number and Cytomegalovirus Promoter Methylation in Transgenic Pigs

Transgenic animals have been used for years to study gene function, produce important proteins, and generate models for the study of human diseases. However, inheritance and expression instability of the transgene in transgenic animals is a major limitation. Copy number and promoter methylation are known to regulate gene expression, but no report has systematically examined their effect on transgene expression. In the study, we generated two transgenic pigs by somatic cell nuclear transfer (SCNT) that express green fluorescent protein (GFP) driven by cytomegalovirus (CMV). Absolute quantitative real-time PCR and bisulfite sequencing were performed to determine transgene copy number and promoter methylation level. The correlation of transgene expression with copy number and promoter methylation was analyzed in individual development, fibroblast cells, various tissues, and offspring of the transgenic pigs. Our results demonstrate that transgene expression is associated with copy number and CMV promoter methylation in transgenic pigs