495 research outputs found
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 of integrated luminosity collected with the D0 detector
at the Fermilab Tevatron collider. We search for events in which one
or more particles are reconstructed as muons but have speed and ionization
energy loss 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
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