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Search Results: 1 - 10 of 325503 matches for " Boian S. Alexandrov "
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Robust accidental nodes and zeroes and critical quasiparticle scaling in iron-based multiband superconductors
Valentin Stanev,Boian S. Alexandrov,Predrag Nikolic,Zlatko Tesanovic
Physics , 2010, DOI: 10.1103/PhysRevB.84.014505
Abstract: We study multigap superconductivity, with strong angular variations of one of the gaps, as appropriate for certain iron-based high-temperature superconductors. We solve the gap equations of this model and find that the nodes or zeroes in the gap function present at Tc - although purely accidental -- typically survive down to T=0. Based on this result, we investigate the line of quantum transitions at which gap zeroes first appear. The peculiar "zero-point" critical scaling emanating from this line dominates quasiparticle thermodynamics and transport properties over much of the phase diagram, and supplants more familiar forms of scaling associated with accidental nodes.
Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter
Boian S. Alexandrov ,Vladimir Gelev ,Sang Wook Yoo,Alan R. Bishop,Kim ?. Rasmussen,Anny Usheva
PLOS Computational Biology , 2009, DOI: 10.1371/journal.pcbi.1000313
Abstract: Establishing the general and promoter-specific mechanistic features of gene transcription initiation requires improved understanding of the sequence-dependent structural/dynamic features of promoter DNA. Experimental data suggest that a spontaneous dsDNA strand separation at the transcriptional start site is likely to be a requirement for transcription initiation in several promoters. Here, we use Langevin molecular dynamic simulations based on the Peyrard-Bishop-Dauxois nonlinear model of DNA (PBD LMD) to analyze the strand separation (bubble) dynamics of 80-bp-long promoter DNA sequences. We derive three dynamic criteria, bubble probability, bubble lifetime, and average strand separation, to characterize bubble formation at the transcriptional start sites of eight mammalian gene promoters. We observe that the most stable dsDNA openings do not necessarily coincide with the most probable openings and the highest average strand displacement, underscoring the advantages of proper molecular dynamic simulations. The dynamic profiles of the tested mammalian promoters differ significantly in overall profile and bubble probability, but the transcriptional start site is often distinguished by large (longer than 10 bp) and long-lived transient openings in the double helix. In support of these results are our experimental transcription data demonstrating that an artificial bubble-containing DNA template is transcribed bidirectionally by human RNA polymerase alone in the absence of any other transcription factors.
DNA Dynamics Is Likely to Be a Factor in the Genomic Nucleotide Repeats Expansions Related to Diseases
Boian S. Alexandrov,Vlad I. Valtchinov,Ludmil B. Alexandrov,Vladimir Gelev,Yossi Dagon,Jonathan Bock,Isaac S. Kohane,Kim ?. Rasmussen,Alan R. Bishop,Anny Usheva
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019800
Abstract: Trinucleotiderepeats sequences (TRS) represent a common type of genomic DNA motif whose expansion is associated with a large number of human diseases. The driving molecular mechanisms of the TRS ongoing dynamic expansion across generations and within tissues and its influence on genomic DNA functions are not well understood. Here we report results for a novel and notable collective breathing behavior of genomic DNA of tandem TRS, leading to propensity for large local DNA transient openings at physiological temperature. Our Langevin molecular dynamics (LMD) and Markov Chain Monte Carlo (MCMC) simulations demonstrate that the patterns of openings of various TRSs depend specifically on their length. The collective propensity for DNA strand separation of repeated sequences serves as a precursor for outsized intermediate bubble states independently of the G/C-content. We report that repeats have the potential to interfere with the binding of transcription factors to their consensus sequence by altered DNA breathing dynamics in proximity of the binding sites. These observations might influence ongoing attempts to use LMD and MCMC simulations for TRS–related modeling of genomic DNA functionality in elucidating the common denominators of the dynamic TRS expansion mutation with potential therapeutic applications.
Mammalian Stem Cells Reprogramming in Response to Terahertz Radiation
Jonathan Bock,Yayoi Fukuyo,Sona Kang,M. Lisa Phipps,Ludmil B. Alexandrov,Kim ?. Rasmussen,Alan R. Bishop,Evan D. Rosen,Jennifer S. Martinez,Hou-Tong Chen,George Rodriguez,Boian S. Alexandrov,Anny Usheva
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015806
Abstract: We report that extended exposure to broad-spectrum terahertz radiation results in specific changes in cellular functions that are closely related to DNA-directed gene transcription. Our gene chip survey of gene expression shows that whereas 89% of the protein coding genes in mouse stem cells do not respond to the applied terahertz radiation, certain genes are activated, while other are repressed. RT-PCR experiments with selected gene probes corresponding to transcripts in the three groups of genes detail the gene specific effect. The response was not only gene specific but also irradiation conditions dependent. Our findings suggest that the applied terahertz irradiation accelerates cell differentiation toward adipose phenotype by activating the transcription factor peroxisome proliferator-activated receptor gamma (PPARG). Finally, our molecular dynamics computer simulations indicate that the local breathing dynamics of the PPARG promoter DNA coincides with the gene specific response to the THz radiation. We propose that THz radiation is a potential tool for cellular reprogramming.
Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics
Kristy Nowak-Lovato,Ludmil B. Alexandrov,Afsheen Banisadr,Amy L. Bauer,Alan R. Bishop,Anny Usheva,Fangping Mu,Elizabeth Hong-Geller,Kim ?. Rasmussen,William S. Hlavacek ,Boian S. Alexandrov
PLOS Computational Biology , 2013, DOI: 10.1371/journal.pcbi.1002881
Abstract: Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications.
The effective action and quantum gauge transformations
S. Alexandrov
Physics , 1998, DOI: 10.1103/PhysRevD.59.125016
Abstract: The local symmetry transformations of the quantum effective action for general gauge theory are found. Additional symmetries arise under consideration of background gauges. Together with "trivial" gauge transformations, vanishing on mass shell, they can be used for construction simple gauge generators. For example, for the Yang-Mills theory the classically invariant effective action is obtained, reproducing DeWitt's result. For rank one theories a natural generalization is proposed.
Boson-fermion model beyond mean-field approximation
A. S. Alexandrov
Physics , 1996, DOI: 10.1088/0953-8984/8/37/014
Abstract: A model of hybridized bosons and fermions is studied beyond the mean field approximation. The divergent boson self-energy at zero temperature makes the Cooper pairing of fermions impossible.The frequency and momentum dependence of the self- energy and the condensation temperature $T_{c}$ of initially localized bosons are calculated analytically. The value of the boson condensation temperature $T_{c}$ is below $1K$ which rules out the boson-fermion model with the initially localized bosons as a phenomenological explanation of high-temperature superconductivity. The intra-cell density-density fermion-boson interaction dominates in the fermion self-energy. The model represents a normal metal with strongly damped bosonic excitations. The latter play the role of normal impurities.
Logarithmic divergence of normal state resistivity of bipolaronic high-$T_{c}$ cuprates
A. S. Alexandrov
Physics , 1996,
Abstract: The resonance Wigner scattering of charged bosons (small bipolarons) in a random potential leads to logarithmically divergent low-temperature resistivity as observed in several cuprates. Unusual temperature dependence of resistivity of $La_{2-x}Sr_{x}CuO_{4}$ as well as of the Hall effect is quantitatively described in a wide temperature range providing an evidence for $2e$ charged Bose-liquid in high-$T_{c}$ cuprates.
Theory of tunnelling into and from cuprates
A. S. Alexandrov
Physics , 1998,
Abstract: A single-particle spectral density is proposed for cuprates taking into account the bipolaron formation, realistic band structure, thermal fluctuations and disorder. Tunnelling and photoemission (PES) spectra are described, including the temperature independent gap observed both in the superconducting and normal states, the emission/injection asymmetry, the finite zero-bias conductance, the spectral shape in the gap region and its temperature and doping dependence, dip-hump incoherent asymmetric features at high voltage (tunnelling) and large binding energy (PES).
Comment on `Experimental and Theoretical Constraints of Bipolaronic Superconductivity in High $T_{c}$ Materials: An Impossibility'
A. S. Alexandrov
Physics , 1998, DOI: 10.1103/PhysRevLett.82.2620
Abstract: We show that objections raised by Chakraverty $et$ $al$ (Phys. Rev. Lett. 81, 433 (1998)) to the bipolaron model of superconducting cuprates are the result of an incorrect approximation for the bipolaron energy spectrum and misuse of the bipolaron theory. The consideration, which takes into account the multiband energy structure of bipolarons and the unscreened electron-phonon interaction clearly indicates that cuprates are in the Bose-Einstein condensation regime with mobile charged bosons.
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