Hydration of a B-DNA Fragment in the Method of Atom-atom Correlation Functions with the Reference Interaction Site Model Approximation

We propose an efficient numerical algorithm for solving integral equations of the theory of liquids in the Reference Interaction Site Model (RISM) approximation for infinitely dilute solution of macromolecules with a large number of atoms. The algorithm is based on applying the nonstationary iterative methods for solving systems of linear algebraic equations. We calculate the solvent-solute atom-atom correlation functions for a fragment of the B-DNA duplex d(GGGGG).d(CCCCC) in infinitely dilute aqueous solution. The obtained results are compared with available experimental data and results from computer simulations.Comment: 9 pages, RevTeX, 9 pages of ps figures, accepted for publications in JC

On a classification of E. coli promoters according to their electrostatic potential

Classiˇcation of promoters and other functionally important genome fragments according to their nucleotide sequences and physicochemical properties is a key factor for understanding gene transcription, replication, recombination and their regulation. The classiˇcation of genome promoters is usually performed on the basis of analysis of their primary structures. However, such an approach does not allow one to obtain a simple answer because it is the physicochemical properties of DNA that control the process of gene transcription and its regulation. Electrostatic interactions comprise an essential component of those processes. This work presents the approach that allows computation of electrostatic potentials of long nucleotide sequences of DNA for both procaryotic and eucaryotic species. The elecrtostatic potentials of E. coli promoters and periodic sequences were calculated. We suppose that the electrostatic characteristics of the genome promoters together with primary structure provide their reliable classiˇcation. Š² ¸¸¨Ë¨± ꬅ ¶·µ³µÉµ·µ¢¨¤·Ê£¨Ì ËÊ´±Í¨µ´ ²Ó´µ ¢ ¦´ÒÌ Ô²¥³¥´Éµ¢ £¥´µ³ ¶µ¨Ì´Ê±²¥µ-ɨ¤´Ò³ ¶µ¸²¥¤µ¢ É¥²Ó´µ¸ÉÖ³¨Ë¨ §¨±µ-̨³¨Î¥¸±¨³¸¢µ°¸É¢ ³ Ö¢²Ö¥É¸Ö ±²ÕÎ¥¢Ò³ Ë ±Éµ·µ³ ¤²Ö ¶µ´¨³ ´¨Ö ¶·µÍ¥¸¸µ¢ É· ´¸±·¨ ¶Í¨¨£¥´µ¢, ·¥¤Ê ¶²¨± ͨ¨, ·¥±µ³¡¨´ ͨ¨¨¨Ì ·¥£Ê²Öͨ¨. ¡Òδµ ±² ¸¸¨Ë¨± ꬅ ¶·µ³µÉµ·µ¢ £¥´µ³ ¶·µ¢µ¤¨É¸Ö´ µ¸´µ¢¥ ´ ²¨ § ¨Ì ¶¥·¢¨Î´Ò̸ɷʱÉÊ·. ¤´ ±µ É ±µ° ¶µ¤Ìµ¤´¥ ¶µ §¢µ²Ö¥É ¶µ²ÊΨÉÓ µ¤´µ §´ δµ£µ µÉ¢¥É , É. ±. § ¶·µÍ¥¸¸É· ´¸±·¨ ¶Í¨¨¨¥¥ ·¥-£Ê²ÖÍ¨Õ ¢ µ¸´µ¢´µ³ µÉ¢¥É¸É¢¥´´Ò ˨ §¨±µ-̨³¨Î¥¸±¨¥¸¢µ°¸É¢ "Š. ‚ ¦´ÊÕ ·µ²Ó ¢ ʱ § ´´ÒÌ ¶·µÍ¥¸¸ ̨£· ÕÉ Ô²¥±É·µ¸É ɨΥ¸±¨¥ ¢ § ¨³µ¤¥°¸É¢¨Ö. ‚´ ¸ÉµÖÐ¥°· ¡µÉ¥ · §¢¨É ¶µ¤Ìµ¤, ¶µ §¢µ-²ÖÕШ°¢ÒΨ¸²ÖÉÓ Ô²¥±É·µ¸É ɨΥ¸±¨¥ ¶µÉ¥´Í¨ ²Ò ¤²¨´´Ò̴ʱ²¥µÉ¨¤´ÒÌ ¶µ¸²¥¤µ¢ É¥²Ó´µ¸É¥°" Š ± ± ¤²Ö ¶·µ± ·¨µÉ, É ±¨¤²Ö Ôʱ ·¨µÉ. ³¨¢ÒΨ¸²¥´Ò Ô²¥±É·µ¸É ɨΥ¸±¨¥ ¶µÉ¥´Í¨ ²Ò ¶·µ³µÉµ·µ¢ E. coli¨ ¶¥·¨µ¤¨Î¥¸±¨Ì ¶µ¸²¥¤µ¢ É¥²Ó´µ¸É¥°. OEÒ ¶µ² £ ¥³, Îɵ Ô²¥±É·µ¸É ɨΥ¸±¨¥ Ì · ±É¥·¨¸É¨±¨ ¶·µ³µÉµ·µ¢ £¥´µ³ ¸µ¢³¥¸É´µ¸ ¶¥·¢¨Î´µ°¸É·Ê±ÉÊ·µ°µ¡¥¸ ¶¥Î ɨ̴ ¤¥¦´ÊÕ ±² ¸¸¨Ë¨± ͨÕ

High-Q trenched aluminum coplanar resonators with an ultrasonic edge microcutting for superconducting quantum devices

Dielectric losses are one of the key factors limiting the coherence of superconducting qubits. The impact of materials and fabrication steps on dielectric losses can be evaluated using coplanar waveguide (CPW) microwave resonators. Here, we report on superconducting CPW microwave resonators with internal quality factors systematically exceeding 5x106 at high powers and 2x106 (with the best value of 4.4x106) at low power. Such performance is demonstrated for 100-nm-thick aluminum resonators with 7-10.5 um center trace on high-resistivity silicon substrates commonly used in quantum Josephson junction circuits. We investigate internal quality factors of the resonators with both dry and wet aluminum etching, as well as deep and isotropic reactive ion etching of silicon substrate. Josephson junction compatible CPW resonators fabrication process with both airbridges and silicon substrate etching is proposed. Finally, we demonstrate the effect of airbridges positions and extra process steps on the overall dielectric losses. The best quality fa ctors are obtained for the wet etched aluminum resonators and isotropically removed substrate with the proposed ultrasonic metal edge microcutting.Comment: 6 pages, 2 figure

Robust cryogenic matched low-pass coaxial filters for quantum computing applications

Electromagnetic noise is one of the key external factors decreasing superconducting qubits coherence. Matched coaxial filters can prevent microwave and IR photons negative influence on superconducting quantum circuits. Here, we report on design and fabrication route of matched low-pass coaxial filters for noise-sensitive measurements at milliKelvin temperatures. A robust transmission coefficient with designed linear absorption (-1dB/GHz) and ultralow reflection losses less than -20 dB up to 20 GHz is achieved. We present a mathematical model for evaluating and predicting filters transmission parameters depending on their dimensions. It is experimentally approved on two filters prototypes different lengths with compound of Cu powder and Stycast commercial resin demonstrating excellent matching. The presented design and assembly route are universal for various compounds and provide high repeatability of geometrical and microwave characteristics. Finally, we demonstrate three filters with almost equal reflection and transmission characteristics in the range from 0 to 20 GHz, which is quite useful to control multiple channel superconducting quantum circuits.Comment: 5 pages, 4 figure

A method for identification of the methylation level of CpG islands from NGS data

In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data

Antitumor features of Bacillus oligonitrophilus KU-1 strain

Chemotherapy and radiotherapy remain mostly palliative methods for metastatic cancer treatment. Limitations in efficacy and safety of established treatments continue to underline the need for improved treatments for malignancy. Results with some probiotics with antitumor activity have been promising. Here, we report that oral reception of Bacillus oligonitrophilus KU-1 resulted in the prolongation of lives in cancer patients with terminal prognosis and stabilization of cancer growth. The theoretical basis for the phenomena observed is discussed

A search for charged massive long-lived particles

We report on a search for charged massive long-lived particles (CMLLPs), based on 5.2 fb$^{-1}$ of integrated luminosity collected with the D0 detector at the Fermilab Tevatron $p\bar{p}$ collider. We search for events in which one or more particles are reconstructed as muons but have speed and ionization energy loss $(dE/dx)$ inconsistent with muons produced in beam collisions. CMLLPs are predicted in several theories of physics beyond the standard model. We exclude pair-produced long-lived gaugino-like charginos below 267 GeV and higgsino-like charginos below 217 GeV at 95% C.L., as well as long-lived scalar top quarks with mass below 285 GeV.Comment: submitted to Phys. Rev. Letter

Precise measurement of the top quark mass in the dilepton channel at D0

We measure the top quark mass (mt) in ppbar collisions at a center of mass energy of 1.96 TeV using dilepton ttbar->W+bW-bbar->l+nubl-nubarbbar events, where l denotes an electron, a muon, or a tau that decays leptonically. The data correspond to an integrated luminosity of 5.4 fb-1 collected with the D0 detector at the Fermilab Tevatron Collider. We obtain mt = 174.0 +- 1.8(stat) +- 2.4(syst) GeV, which is in agreement with the current world average mt = 173.3 +- 1.1 GeV. This is currently the most precise measurement of mt in the dilepton channel.Comment: 7 pages, 4 figure