pinecone/core-2020-05-10-deduplication huggingface dataset:
Fermi's golden rule in a mesoscopic metal ring

We examine the time-dependent non-equilibrium current in a mesoscopic metal
ring threaded by a static magnetic flux phi that is generated by a
time-dependent electric field oscillating with frequency omega. We show that in
quadratic order in the field there are three fundamentally different
contributions to the current. (a) A time-independent contribution which can be
obtained from a thermodynamic derivative. (b) A term increasing linearly in
time that can be understood in terms of Fermi's golden rule. The derivation of
this term requires a careful treatment of the infinitesimal imaginary parts
that are added to the real frequency omega when the electric field is
adiabatically switched on. (c) Finally, there is also a time-dependent current
oscillating with frequency 2 omega. We suggest an experiment to test our
results.Comment: this is an expanded and completely revised version of our withdrawn
  manuscript cond-mat/971230
Shrinking limits of silicon MOSFET's: Numerical study of 10-nm-scale
  devices

We have performed numerical modeling of dual-gate ballistic n-MOSFET's with
channel length of the order of 10 nm, including the effects of quantum
tunneling along the channel and through the gate oxide. Our analysis includes a
self-consistent solution of the full (two-dimensional) electrostatic problem,
with account of electric field penetration into the heavily-doped electrodes.
The results show that transistors with channel length as small as 8 nm can
exhibit either a transconductance up to 4,000 mS/mm or gate modulation of
current by more than 8 orders of magnitude, depending on the gate oxide
thickness. These characteristics make the devices satisfactory for logic and
memory applications, respectively, though their gate threshold voltage is
rather sensitive to nanometer-scale variations in the channel length.Comment: 8 pages, 10 figures. Submitted to Special Issue of Superlattices and
  Microstructures: Third NASA Workshop on Device Modeling, August 199
Contact resistance of quantum tubes

We consider the conductance of a quantum tube connected to a metallic
contact. The number of angular momentum states that the tube can support
depends on the strength of the radial confinement. We calculate the
transmission coefficients which yield the conductance via the Landauer formula.
We relate our results to armchair carbon nanotubes embedded in a metal. For Al
and Au contacts and tubes with a realistic radial confinement we find that the
transmission can be close to unity corresponding to a contact resistance close
to h/2e^2 per band at the Fermi level in the carbon nanotube.Comment: 13 pages including 5 figures. Accepted for publication in
  Superlattices and Microstructures. (stylefile included
Supression of magnetic subbands in semiconductor superlattices driven by
  a laser field

The effect of strong laser radiation on magnetic subbands in semiconductor
superlattices is investigated. Due to the presence of a magnetic field
perpendicular to the growth direction, non-linear effects such as band
supression and electron localization become relevant at relatively lower
intensities and for any polarization perpendicular to the magnetic field.
Electron quasienergies and density of states are calculated in the
Kramers-Henneberger approximation, whose validity is discussed. The conditions
under which collapse of magnetic subbands and quenching of N-photon emission or
absorption processes occur are discussed. We conclude that at laser frequencies
close to cyclotronic frequency and intensities typical of c.w. lasers, magnetic
subbands become flat, magnetotunneling is inhibited and multiphotonic processes
dominate optical absorption.Comment: 4 pages RevTex, 2 figure
Spintronics: electron spin coherence, entanglement, and transport

Prospect of building spintronic devices in which electron spins store and
transport information has attracted strong attention in recent years. Here we
present some of our representative theoretical results on three fundamental
aspects of spintronics: spin coherence, spin entanglement, and spin transport.
In particular, we discuss our detailed quantitative theory for spin relaxation
and coherence in electronic materials, resolving in the process a long-standing
puzzle of why spin relaxation is extremely fast in Al (compared with other
simple metals). In the study of spin entanglement, we consider two electrons in
a coupled GaAs double-quantum-dot structure and explore the Hilbert space of
the double dot. The specific goal is to critically assess the quantitative
aspects of the proposed spin-based quantum dot quantum computer architecture.
Furthermore, we discuss our theory of spin-polarized transport across a
semiconductor-metal interface. In particular, we study Andreev reflection,
which enables us to quantify the degree of carrier spin polarization and the
strength of interfacial scattering.Comment: 9 pages and 3 eps figures. To appear in the proceedings of the
  Surfaces and Interfaces of Mesoscopic Devices 99. Acknowledgment adde
Dephasing in semiconductor-superconductor structures by coupling to a
  voltage probe

We study dephasing in semiconductor-superconductor structures caused by
coupling to a voltage probe. We consider structures where the semiconductor
consists of two scattering regions between which partial dephasing is possible.
As a particular example we consider a situation with a double-barrier junction
in the normal region. For a single-mode system we study the conductance both as
a function of the position of the Fermi level and as a function of the barrier
transparency. At resonance, where the double-barrier is fully transparent, we
study the suppression of the ideal factor-of-two enhancement of the conductance
when a finite coupling to the voltage probe is taken into account.Comment: 13 pages including 3 figures. Accepted for publication in
  Superlattices and Microstructure
Side-gate modulation of critical current in mesoscopic Josephson
  junction

We study the normal state conductance and the Josephson current in a
superconductor-2DEG-superconductor structure where the size/shape of the
2DEG-region can be modified by an additional side-gate electrode. The
considered transport properties follow from the retarded Green function which
we compute by employing a tight-binding-like representation of the Hamiltonian
in the 2DEG region. Our model studies offer a qualitative demonstration of the
recently observed effects caused by side-gate modulation.Comment: 9 pages including 4 figures. Reference to cond-mat/0005435 adde
Model calculations of the proximity effect in finite multilayers

The proximity-effect theory developed by Takahashi and Tachiki for infinite
multilayers is applied to multilayer systems with a finite number of layers in
the growth direction. The purpose is to investigate why previous applications
to infinite multilayers fail to describe the measured data satisfactorily.
Surface superconductivity may appear, depending on the thickness of the
covering normal metallic N layers on both the top and the bottom. The
parameters used are characteristic for V/Ag and Nb/Pd systems. The nucleation
process is studied as a function of the system parameters.Comment: 12 pages, 15 figures, RevTe
A Stochastic Metapopulation Model with Variability in Patch Size and Position

Analytically tractable metapopulation models usually assume that every patch is identical, which limits their application to real metapopulations. We describe a new single species model of metapopulation dynamics that allows variation in patch size and position. The state of the metapopulation is defined by the presence or absence of the species in each patch. For a system of n patches, this gives 2^n possible states. We show how to construct and analyse a matrix describing transitions between all possible states by first constructing separate extinction and colonisation matrices. We illustrate the model\u27s application to metapopulations by considering an example of malleefowl, Leipoa ocellata, in southern Australia, and calculate extinction probabilities and quasi-stationary distributions. We investigate the relative importance of modelling the particular arrangement of patches and the variation in patch sizes for this metapopulation and we use the model to examine the effects of further habitat loss on extinction probabilities
Gene 2 of the Sigma Rhabdovirus Genome Encodes the P Protein, and Gene 3 Encodes a Protein Related to the Reverse Transcriptase of Retroelements

AbstractThe nucleotide sequence of the genes 2 and 3 of theDrosophilarhabdovirus sigma was determined from cDNAs to viral genome and poly(A)+mRNAs. Gene 2 comprises 1032 nucleotides and contains a long ORF encoding a molecular weight 35,208 polypeptide present in infected cells and in virions which migrates in SDS–PAGE as a doublet ofMrabout 60 kDa. The distribution of acidic charges as well as the electrophoretic properties of the protein are characteristic of the rhabdovirus P proteins. Gene 3 comprises 923 nucleotides and contains a long ORF capable of coding a polypeptide of 298 amino acids of MW 33,790. The putative protein (PP3) is similar in size to a minor component of the virions. Computer analysis shows that the sequence of PP3 contains three motifs related to the conserved motifs of reverse transcriptases
Immunological Adenovirus Variant Strains of Subgenus D: Comparison of the Hexon and Fiber Sequences

AbstractThe fiber and hexon genes of the immunological adenovirus (Ad) variant strains Ad9/Hx and Ad15/Hx, belonging to subgenus D, were sequenced and compared to the corresponding sequences of the prototypes Ad9 and Ad15. It was found that the variants possessed a novel and identical hemagglutinin as they could not be distinguished by hemagglutination-inhibition tests. These serological data were now confirmed on DNA and protein level. The analyzed hexon regions of Ad15 and Ad15/Hx, and Ad9 and Ad9/Hx, respectively, were 100% identical on the amino acid level. The comparison between the variant fibers revealed that they possessed an identical fiber, which was distinct from the Ad9 and Ad15 fiber polypeptides. It seems likely that the donor of the novel fiber protein was a so far unidentified subgroup D adenovirus. The fiber polypeptides of Ad9 and the variants revealed the highest homology (73.7%), whereas the variants and the Ad15 fiber had only 64.2% of the amino acids in common. Most of the differences between the adenovirus serotypes were detected in the fiber knob. Seven conserved sequences found for subgenus D fibers could be confirmed for the fibers of the variants. Furthermore, the data presented complement the knowledge on the organization of subgenus D fiber genes
Sequences Required for the Nuclear Targeting and Accumulation of Human Papillomavirus Type 6B L2 Protein

AbstractThe L2 protein of the human papillomaviruses is a minor structural protein and is not necessary for the major L1 protein to assemble into capsids. However L2 protein binds DNA and enhances the efficiency of HPV capsid assembly, suggesting an important role in the production of infectious papillomaviruses. L2 accumulates rapidly in the nucleus after synthesis in the cytoplasm. To identify L2 sequences responsible for nuclear targeting and accumulation, full-length HPV6bL2 protein and L2 proteins containing sequence deletions were expressed in CV-1 cells, using recombinant vaccinia viruses. βgal protein fused to C-terminal and N-terminal L2 sequences were localized in the nucleus and demonstrated that both the C-terminal putative nuclear localization signal (NLS) and N-terminal DNA binding sequences of the L2 protein, which are rich in arginine and lysine, are functional in targeting proteins into the nucleus. L2 mutants lacking amino acids (aa 286–306) do not accumulate in nucleus even when the C-terminal NLS and N-terminal DNA binding sequences are intact. Accumulation in the nucleus of L2 protein lacking aa 286–306 could be also achieved by increasing the L2 protein size via insertion of a portion of L1 protein. Amino acid sequence alignment of L2 proteins from sequenced papillomaviruses showed that sequences in this region are relatively conserved. Our results indicate that in the L2 protein, the nuclear targeting and accumulation are controlled by two different sequences and the rapid nuclear translocation and accumulation may play an important role in papillomavirus life cycle
The Replicationin Vitroof the Gammaherpesvirus Bovine Herpesvirus 4 Is Restricted by Its DNA Synthesis Dependence on the S Phase of the Cell Cycle

AbstractBecause several observations have suggested that replication of the gammaherpesvirus bovine herpesvirus 4 (BHV-4) is influenced by the physiological state of the host cell, a study was carried out to determine the relationship between BHV-4 infection and the cell cycle. The temporal expression of BHV-4 late (L) proteins in unsynchronized cell cultures was first investigated by flow cytometry. Interestingly, L protein expression occurred in a limited number of cells infected with a high multiplicity of infection, and a reciprocal correlation between the percentage of positive cells and the cell density at the time of infection was demonstrated. Moreover, the finding that a BHV-4 early–late protein was expressed in nearly all the cells suggested that a blockage in the viral replication cycle occurred in some infected cells at the stage of viral DNA synthesis or L protein expression. Because this blockage could be the consequence of the dependence of one or both of these events on the cell cycle, they were investigated after infection of synchronized cell cultures. The following findings were made. (i) Cell transition through the S phase quantitatively increased the rate of BHV-4 DNA replication. (ii) BHV-4 DNA synthesis could not be detected in cells arrested in G0. (iii) Synchronization of MDBK cells with Lovastatin before infection increased the percentage of cells expressing L proteins. (iv) In contrast, infection of cells arrested in G0led to few positive cells. Taken together these results showed that BHV-4 DNA replication and consequently the expression of L proteins are dependent on the S phase of the cell cycle. This dependence could be of importance for several biological properties of BHV-4 infectionin vitroand might have implications for the biology of the virusin vivo
Sequence of the M28 dsRNA: Preprotoxin Is Processed to an α/β Heterodimeric Protein Toxin

AbstractThe killer and immunity phenotypes of K28 killer strains ofSaccharomyces cerevisiaeare determined by the 1.75-kb M28 dsRNA virus. In the plus strand, M28p, the K28 preprotoxin gene, comprises bases 13–1047 and is followed, after an additional 85 bases, by a 63-bp poly(A) sequence and a 553-base 3′-sequence. This 3′-sequence contains two potential stem–loop structures predicted to bind the L-A encoded cap–pol protein, initiating encapsidation; high-level expression results in curing of M1 dsRNA. Expression of M28p confers the complete K28 killer and immunity phenotype on a cell lacking M28 dsRNA. K28 toxin is a disulfide-bonded heterodimer of α (10.5 kDa) and β (11 kDa) components whose N-termini correspond to M28p residues 50–61 and 246–257, respectively. α is preceded by a potentially redundant pair of secretion signal peptides; deletion of the first reduces toxin secretion by 75%. While M28p bears no sequence similarity to M1p, the K1 preprotoxin, the predicted patterns of processing by glycosylation and cleavage are remarkably similar. The β N- and C-termini are probably processed by Kex2p and Kex1p, respectively; the mechanism of cleavage at the less typical sites bounding the α component is under investigation. While akex2Δ mutation prevents toxin secretion, secreted toxin retains 20% activity in akex1Δ mutant. Neither mutation affects immunity
Mutations in Conserved Domain I of the Sendai Virus L Polymerase Protein Uncouple Transcription and Replication

AbstractTo begin to map functional domains of the Sendai P-L RNA polymerase complex we wanted to characterize the P binding site on the Sendai L protein. Analysis ofin vitroandin vivoP-L polymerase complex formation with carboxyl-truncations of the L protein showed that the N-terminal half of the protein was required. Site-directed mutagenesis of the Sendai virus L gene was employed to change amino acids within a highly conserved region of the N-terminal domain I from amino acids (aa) 348–379 singly or in pairs from the Sendai to the corresponding measles L sequence or to alanine. The mutant L proteins coexpressed with the viral P and NP proteins in mammalian cells were assayed for their ability to form the P-L complex and to synthesize RNAin vitroand showed a variety of defective phenotypes. While most of the mutant L proteins still formed the P-L polymerase complex, a change from serine to arginine at aa 368 and a three-amino-acid insertion at aa 379 virtually abolished both complex formation and RNA synthesis. Changes of aas 370 and 376–377 in the L protein gave only small decreases in viral RNA synthesis. Substitutions at either aas 349–350 or aas 354–355 and a three-amino-acid insertion at aa 348 in the L protein yielded enzymes that catalyzed significant transcription, but were defective in DI RNA replication, thus differentially affecting the two processes. Since DI leader RNA, but not genome RNA, was still synthesized by this class of mutants, the defect in replication appears to be in the ability of the mutant enzyme to package newly synthesized nascent RNA. Single changes at aas 362, 363, and 366 in the L protein gave enzymes with severely decreased overall RNA synthesis, although some leader RNA was synthesized, suggesting that they cannot transcribe or replicate past the leader gene. These studies have identified a region in conserved domain I critical for multiple functions of the Sendai virus L protein
Equine Arteritis Virus Subgenomic RNA Transcription: UV Inactivation and Translation Inhibition Studies

AbstractThe expression of the genetic information of equine arteritis virus (EAV), an arterivirus, involves the synthesis of six subgenomic (sg) mRNAs. These are 5′ and 3′ coterminal since they are composed of a leader and a body sequence, which are identical to the 5′ and 3′ ends of the genome, respectively. Previously, it has been suggested thatcis-splicing of a genome-length precursor RNA is involved in their synthesis. This was reevaluated in a comparative analysis of the sg RNA synthesis of EAV, the coronavirus mouse hepatitis virus (MHV), and the alphavirus Sindbis virus. UV transcription mapping showed that the majority of the EAV sg RNAs made at later stages of infection is not derived from a genome-length precursor. However, complete independence of sg RNA synthesis from that of genomic RNA was never observed during the course of infection. The possibility that this resulted from UV irradiation-induced effects on the synthesis of the viral replicase was investigated by inhibiting translation using cycloheximide. For EAV, ongoing protein synthesis was found to be more important for the synthesis of sg RNA than for that of genomic RNA. In general, MHV transcription was extremely sensitive to translation inhibition, whereas EAV genomic RNA synthesis became independent ofde novoprotein synthesis late in infection
Two Strong 5′ Splice Sites and Competing, Suboptimal 3′ Splice Sites Involved in Alternative Splicing of Human Immunodeficiency Virus Type 1 RNA

AbstractThe human immunodeficiency virus type 1 (HIV-1) genome contains 20 exons that are alternatively spliced from 16 splice sites to generate more than 40 different mRNAs, including incompletely spliced and unspliced mRNAs. In contrast to avian retroviral RNA, which has acis-acting element ingagthat negatively regulates splicing (NRS), HIV-1 RNA did not have any NRS sequences in thegagorpolgenes detectable by a splicing inhibition assay. However, this assay demonstrated that the HIV-1 first 5′ splice site competed with a cellular 5′ splice site, suggesting that HIV-1 may have some strong splice sites. To extend this observation, we used a splice site swapping strategy to determine the efficiency of 14 HIV-1 splice sites in human β globin chimeras tested in transient transfection experiments. While the 1st HIV-1 5′ splice site used in all spliced transcripts and the 4th 5′ splice site used in most of the 2-kb transcripts were efficient, the other splice sites, including all the 3′ splice sites, were less efficient, ranging in use from 25 to 60%. We propose that this range of splice site efficiencies contributes to the regulation of alternative splicing of HIV-1 mRNAs
Characterization of a CD4-Expressing Macaque Cell Line That Can Detect Virus after a Single Replication Cycle and Can Be Infected by Diverse Simian Immunodeficiency Virus Isolates

AbstractPrimate lentiviruses such as human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) are phenotypically diverse, and virus isolates vary in cytopathicity, replication rate, and cell tropism. While all virus isolates infect primary peripheral blood lymphocytes, only a subset of strains infect established CD4-expressing T-cell lines. Here, we describe the development and characterization of a macaque cell line that can be infected by all of the strains of SIV that we have tested, including macrophage- and T-cell-tropic strains, primary and cell-line adapted strains, and SIVmac, SIVMne, and SIVsm isolates. The cells can be infected by strains of HIV type 2 (HIV-2) to varying degrees, but not by either cloned or primary isolates of HIV type 1 (HIV-1). This cell line is a derivative of a rhesus macaque mammary tumor cell line (CMMT) engineered to express human CD4. For these studies, a CMMT-CD4 clone expressing an integrated copy of a truncated HIV-1 long terminal repeat fused to theβ-galactosidasegene (LTR-β-gal) was established to allow detection of infectious SIV after a single round of replication. Here, we demonstrate the ability of the CMMT-CD4-LTR-β-galcell line to rapidly and quantitatively detect infectious SIV. Using these cells to assay virus, we could readily measure neutralizing antibody activity in animals infected with different SIV isolates. Neutralizing activity was detected against the homologous virus and lower, but detectable, activity was measured against heterologous virus. Thus, this system, which is highly sensitive and can detect infection by all of the SIV isolates we tested, is a rapid method for detecting infectious virus and quantitating neutralizing antibody activity