Statistical Mechanics of DNA Rupture: Theory and Simulations

We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the rupture force. We obtain a significant difference between the atomistic simulations and the existing results in the iterature based on the coarse-grained models (theory and simulations). We discuss the possible reasons and improve the coarse-grained model by incorporating the consequences of semi-microscopic details of the nucleotides in its description. The distributions obtained by the modified model (simulations and theoretical) are qualitatively similar to the one obtained using atomistic simulations.Comment: 18 pages, 9 figures. Accepted in J. Chem. Phys. (2013). arXiv admin note: text overlap with arXiv:1104.305

Bone mineral density in patients with inherited bone marrow failure syndromes.

BackgroundPatients with inherited bone marrow failure syndromes (IBMFS) may have several risk factors for low bone mineral density (BMD). We aimed to evaluate the prevalence of low BMD in IBMFS and determine the associated risk factors.MethodsPatients with IBMFS with at least one dual-energy X-ray absorptiometry (DXA) scan were evaluated. Diagnosis of each IBMFS, Fanconi anemia (FA), dyskeratosis congenita, Diamond-Blackfan anemia, and Shwachman-Diamond syndrome was confirmed by syndrome-specific tests. Data were gathered on age, height, and clinical history. DXA scans were completed at the lumbar spine, femoral neck, and forearm. BMD was adjusted for height (HAZ) in children (age ≤20 years). Low BMD was defined as a BMD Z-score and HAZ ≤-2 in adults and children, respectively, in addition to patients currently on bisphosphonate therapy.ResultsNine of thirty-five adults (26%) and eleven of forty children (27%) had low BMD. Adults with FA had significantly lower BMD Z-scores than those with other diagnoses; however, HAZ did not vary significantly in children by diagnosis. Risk factors included hypogonadism, iron overload, and glucocorticoid use.ConclusionsAdults and children with IBMFS have high prevalence of low BMD. Prompt recognition of risk factors and management are essential to optimize bone health

Effects of Molecular Crowding on stretching of polymers in poor solvent

We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the simplest representation of biopolymers in a cell. We show the existence of intermediate states during stretching arising as a consequence of molecular crowding. In the constant distance ensemble the force-extension curves exhibit oscillations. We observe the emergence of two or more peaks in the probability distribution curves signaling the coexistence of different states and indicating that the transition is discontinuous unlike what is observed in the absence of molecular crowding.Comment: 14 pages, 6 figure

Agile SoC Development with Open ESP

ESP is an open-source research platform for heterogeneous SoC design. The platform combines a modular tile-based architecture with a variety of application-oriented flows for the design and optimization of accelerators. The ESP architecture is highly scalable and strikes a balance between regularity and specialization. The companion methodology raises the level of abstraction to system-level design and enables an automated flow from software and hardware development to full-system prototyping on FPGA. For application developers, ESP offers domain-specific automated solutions to synthesize new accelerators for their software and to map complex workloads onto the SoC architecture. For hardware engineers, ESP offers automated solutions to integrate their accelerator designs into the complete SoC. Conceived as a heterogeneous integration platform and tested through years of teaching at Columbia University, ESP supports the open-source hardware community by providing a flexible platform for agile SoC development.Comment: Invited Paper at the 2020 International Conference On Computer Aided Design (ICCAD) - Special Session on Opensource Tools and Platforms for Agile Development of Specialized Architecture

Effect of FCNC mediated Z boson on lepton flavor violating decays

We study the three body lepton flavor violating (LFV) decays $\mu^- \to e^- e^+ e^-$, $\tau^- \to l_i^- l_j^+ l_j^-$ and the semileptonic decay $\tau \to \mu \phi$ in the flavor changing neutral current (FCNC) mediated $Z$ boson model. We also calculate the branching ratios for LFV leptonic B decays, $B_{d,s} \to \mu e$, $B_{d,s} \to \tau e$, $B_{d,s} \to \tau \mu$ and the conversion of muon to electron in Ti nucleus. The new physics parameter space is constrained by using the experimental limits on $\mu^- \to e^- e^+ e^-$ and $\tau^- \to \mu^- \mu^+ \mu^-$. We find that the branching ratios for $\tau \to eee$ and $\tau \to \mu \phi$ processes could be as large as $\sim {\cal O}(10^{-8})$ and ${\rm Br}B_{d,s} \to \tau \mu, \tau e) \sim {\cal O}(10^{-10})$. For other LFV B decays the branching ratios are found to be too small to be observed in the near future.Comment: 15 pages, 8 figures, typos corrected, one more section added, version to appear in EPJ

The Adsorption and Collapse Transitions in a Linear Polymer Chain near an Attractive Wall

We deduce the qualitative phase diagram of a long flexible neutral polymer chain immersed in a poor solvent near an attracting surface using phenomenological arguments. The actual positions of the phase boundaries are estimated numerically from series expansion up to 19 sites of a self-attracting self avoiding walk in three dimensions. In two dimensions, we calculate analytically phase boundaries in some cases for a partially directed model. Both the numerical as well as analytical results corroborate the proposed qualitative phase diagram.Comment: 8 pages, 8 figures, revte

Heavy Fermion Behavior, Crystalline Electric Field Effects, and Weak Ferromagnetism in SmOs_{4}Sb_{12}

The filled skutterudite compound SmOs_{4}Sb_{12} was prepared in single crystal form and characterized. The SmOs_{4}Sb_{12} crystals have the LaFe_{4}P_{12}-type structure with lattice parameter a = 9.3085 Angstroms. Specific heat measurements indicate a large electronic specific heat coefficient of ~880 mJ/mol K^{2}, from which an enhanced effective mass m^{*} ~ 170 m_{e} is estimated. The specific heat data also suggest crystalline electric field (CEF) splitting of the Sm^{3+} J = 5/2 multiplet into a Gamma_{7} doublet ground state and a Gamma_{8} quartet excited state separated by 37 K. Electrical resistivity rho(T) measurements reveal a decrease in rho(T) below ~50 K that is consistent with CEF splitting of ~33 K between a Gamma_(7) doublet ground state and Gamma_{8} quartet excited state. Specific heat and magnetic susceptibility measurements display a possible weak ferromagnetic transition at ~2.6 K, which could be an intrinsic property of SmOs_4Sb_{12} or possibly due to an unknown impurity phase.Comment: 24 pages, 11 Postscript figures, to be published in Physical Review

Multifractal Behaviour of n-Simplex Lattice

We study the asymptotic behaviour of resistance scaling and fluctuation of resistance that give rise to flicker noise in an {\em n}-simplex lattice. We propose a simple method to calculate the resistance scaling and give a closed-form formula to calculate the exponent, $\beta_L$, associated with resistance scaling, for any n. Using current cumulant method we calculate the exact noise exponent for n-simplex lattices.Comment: Latex, 9 pages including one figur

CP Violation in \tau ->\nu\pi K_S and D->\pi K_S: The Importance of K_S-K_L Interference

The $B$-factories have measured CP asymmetries in the $\tau\to\pi K_S\nu$ and $D\to K_S\pi$ modes. The $K_S$ state is identified by its decay to two pions at a time that is close to the $K_S$ lifetime. Within the Standard Model and many of its extensions, the asymmetries in these modes come from CP violation in $K^0-\bar{K}^0$ mixing. We emphasize that the interference between the amplitudes of intermediate $K_S$ and $K_L$ is as important as the pure $K_S$ amplitude. Consequently, the measured asymmetries depend on the times over which the relevant decay rates are integrated and on features of the experiment.Comment: 4 pages, 4 figure