Pattern Formation in the Inhomogeneous Cooling State of Granular Fluids

We present results from comprehensive event-driven (ED) simulations of nonlinear pattern formation in freely-evolving granular gases. In particular, we focus on the the morphologies of density and velocity fields in the inhomogeneous cooling state (ICS). We emphasize the strong analogy between the ICS morphologies and pattern formation in phase ordering systems with a globally conserved order parameter.Comment: 11 pages, 4 figures. to appear in Europhys. Let

Genetic Correlations in Mutation Processes

We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a critical rate, the underlying tree morphology is almost irrelevant, while mutation rates higher than this critical rate lead to strong tree-dependent correlations. We show analytically that identical critical behavior underlies all multiple point correlations. This behavior generally characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig

Mechanical activation of vinculin binding to talin locks talin in an unfolded conformation

The force-dependent interaction between talin and vinculin plays a crucial role in the initiation and growth of focal adhesions. Here we use magnetic tweezers to characterise the mechano-sensitive compact N-terminal region of the talin rod, and show that the three helical bundles R1-R3 in this region unfold in three distinct steps consistent with the domains unfolding independently. Mechanical stretching of talin R1-R3 enhances its binding to vinculin and vinculin binding inhibits talin refolding after force is released. Mutations that stabilize R3 identify it as the initial mechano-sensing domain in talin, unfolding at ~5 pN, suggesting that 5 pN is the force threshold for vinculin binding and adhesion progression

Fast computation of distance estimators

BACKGROUND: Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n(3)). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n(2). Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications. RESULTS: We give an advanced algorithm for Computing the number of mutational events between DNA sequences which is significantly faster than both Phylip and Paup. Moreover, we give a new method for estimating pairwise distances between sequences which contain ambiguity Symbols. This new method is shown to be more accurate as well as faster than earlier methods. CONCLUSION: Our novel algorithm for Computing distance estimators provides a valuable tool in phylogeny reconstruction. Since the running time of our distance estimation algorithm is comparable to that of most distance methods, the previous bottleneck is removed. All distance methods, such as NJ, require a distance matrix as input and, hence, our novel algorithm significantly improves the overall running time of all distance methods. In particular, we show for real world biological applications how the running time of phylogeny reconstruction using NJ is improved from a matter of hours to a matter of seconds

Recurrent advanced colonic cancer occurring 11 years after initial endoscopic piecemeal resection: a case report

<p>Abstract</p> <p>Background</p> <p>The high frequency of local recurrence occurring after endoscopic piecemeal resection (EPMR) for large colorectal tumors is a serious problem. However, almost all of these cases of local recurrence can be detected within 1 year and cured by additional endoscopic resection. We report a rare case of recurrent advanced colonic cancer diagnosed 11 years after initial EPMR treatment.</p> <p>Case presentation</p> <p>A 65-year-old male was diagnosed with a sigmoid colon lesion following a routine health check-up. Total colonoscopy revealed a 12 mm type 0-Is lesion in the sigmoid colon, which was diagnosed as an adenoma or intramucosal cancer and treated by EPMR in 1996. The post-resection defect was closed completely using metallic endoclips to avoid delayed bleeding. In 2007, at the third follow up, colonoscopy revealed a 20 mm submucosal tumor (SMT) like recurrence at the site of the previous EPMR. The recurrent lesion was treated by laparoscopic assisted sigmoidectomy with lymph node dissection.</p> <p>Conclusion</p> <p>When it is difficult to evaluate the depth and margins of resected tumors following EPMR, it is important that the defect is not closed in order to avoid tumor implantation, missing residual lesions and to enable earlier detection of recurrence. It is crucial that the optimal follow-up protocol for EPMR cases is clarified, particularly how often and for how long they should be followed.</p

High-Tc Superconductivity and Antiferromagnetism in Multilayered Copper Oxides - A New Paradigm of Superconducting Mechanism -

High-temperature superconductivity (HTSC) in copper oxides emerges on a layered CuO2 plane when an antiferromagnetic Mott insulator is doped with mobile hole carriers. We review extensive studies of multilayered copper oxides by site-selective nuclear magnetic resonance (NMR), which have uncovered the intrinsic phase diagram of antiferromagnetism (AFM) and HTSC for a disorder-free CuO2 plane with hole carriers. We present our experimental findings such as the existence of the AFM metallic state in doped Mott insulators, the uniformly mixed phase of AFM and HTSC, and the emergence of d-wave SC with a maximum Tc just outside a critical carrier density, at which the AFM moment on a CuO2 plane disappears. These results can be accounted for by the Mott physics based on the t-J model. The superexchange interaction J_in among spins plays a vital role as a glue for Cooper pairs or mobile spin-singlet pairs, in contrast to the phonon-mediated attractive interaction among electrons established in the Bardeen-Cooper-Schrieffer (BCS) theory. We remark that the attractive interaction for raising the $T_c$ of HTSC up to temperatures as high as 160 K is the large J_in (~0.12 eV), which binds electrons of opposite spins to be on neighboring sites, and that there are no bosonic glues. It is the Coulomb repulsive interaction U(> 6 eV) among Cu-3d electrons that plays a central role in the physics behind high-Tc phenomena. A new paradigm of the SC mechanism opens to strongly correlated electron matter.Comment: 20 pages, 25 figures, Special topics "Recent Developments in Superconductivity" in J. Phys. Soc. Jpn., Published December 26, 201

Patterned growth of InGaN/GaN quantum wells on freestanding GaN grating by molecular beam epitaxy

We report here the epitaxial growth of InGaN/GaN quantum wells on freestanding GaN gratings by molecular beam epitaxy (MBE). Various GaN gratings are defined by electron beam lithography and realized on GaN-on-silicon substrate by fast atom beam etching. Silicon substrate beneath GaN grating region is removed from the backside to form freestanding GaN gratings, and the patterned growth is subsequently performed on the prepared GaN template by MBE. The selective growth takes place with the assistance of nanoscale GaN gratings and depends on the grating period P and the grating width W. Importantly, coalescences between two side facets are realized to generate epitaxial gratings with triangular section. Thin epitaxial gratings produce the promising photoluminescence performance. This work provides a feasible way for further GaN-based integrated optics devices by a combination of GaN micromachining and epitaxial growth on a GaN-on-silicon substrate

Stretching of a polymer below the Theta point

The unfolding of a polymer below the $\theta$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple steps, corresponding to transitions between different minima, in both cases. In the infinite length limit, these intermediate minima have a qualitative effect only in $d=2$. The phase diagram in d=2 is determined using transfer matrix techniques. Energy-entropy and renormalization group arguments are given which predict a qualitatively correct phase diagram and a change of the order of the transition from d=2 to d=3.Comment: 4 pages, 3 eps figure

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach