Direct Coulomb and Exchange Interaction in Artificial Atoms

We determine the contributions from the direct Coulomb and exchange interactions to the total interaction in semiconductor artificial atoms. We tune the relative strengths of the two interactions and measure them as a function of the number of confined electrons. We find that electrons tend to have parallel spins when they occupy nearly degenerate single-particle states. We use a magnetic field to adjust the single-particle state degeneracy, and find that the spin-configurations in an arbitrary magnetic field are well explained in terms of two-electron singlet and triplet states.Comment: 4 pages, 5 figure

Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation

Abstract Background During their lifetime, microbes are exposed to environmental variations, each with its distinct spatio-temporal dynamics. Microbial communities display a remarkable degree of phenotypic plasticity, and highly-fit individuals emerge quite rapidly during microbial adaptation to novel environments. However, there exists a high variability when it comes to adaptation potential, and while adaptation occurs rapidly in certain environmental transitions, in others organisms struggle to adapt. Here, we investigate the hypothesis that the rate of evolution can both increase or decrease, depending on the similarity and complexity of the intermediate and final environments. Elucidating such dependencies paves the way towards controlling the rate and direction of evolution, which is of interest to industrial and medical applications. Results Our results show that the rate of evolution can be accelerated by evolving cell populations in sequential combinations of environments that are increasingly more complex. To quantify environmental complexity, we evaluate various information-theoretic metrics, and we provide evidence that multivariate mutual information between environmental signals in a given environment correlates well with the rate of evolution in that environment, as measured in our simulations. We find that strong positive and negative correlations between the intermediate and final environments lead to the increase of evolutionary rates, when the environmental complexity increases. Horizontal Gene Transfer is shown to further augment this acceleration, under certain conditions. Interestingly, our simulations show that weak environmental correlations lead to deceleration of evolution, regardless of environmental complexity. Further analysis of network evolution provides a mechanistic explanation of this phenomenon, as exposing cells to intermediate environments can trap the population to local neighborhoods of sub-optimal fitness

Electronic structure of rectangular quantum dots

We study the ground state properties of rectangular quantum dots by using the spin-density-functional theory and quantum Monte Carlo methods. The dot geometry is determined by an infinite hard-wall potential to enable comparison to manufactured, rectangular-shaped quantum dots. We show that the electronic structure is very sensitive to the deformation, and at realistic sizes the non-interacting picture determines the general behavior. However, close to the degenerate points where Hund's rule applies, we find spin-density-wave-like solutions bracketing the partially polarized states. In the quasi-one-dimensional limit we find permanent charge-density waves, and at a sufficiently large deformation or low density, there are strongly localized stable states with a broken spin-symmetry.Comment: 8 pages, 9 figures, submitted to PR

Density of a gas of spin polarized fermions in a magnetic field

For a fermion gas with equally spaced energy levels that is subjected to a magnetic field, the particle density is calculated. The derivation is based on the path integral approach for identical particles, in combination with the inversion techniques for the generating function of the static response functions. Explicit results are presented for the ground state density as a function of the magnetic field with a number of particles ranging from 1 to 45.Comment: 9 pages, 8 figures; To appear in Phys. Rev. E on December 1, 2000; e-mail addresses: [email protected], [email protected], [email protected], [email protected]

Beyond directed evolution: Darwinian selection as a tool for synthetic biology

Synthetic biology is an engineering approach that seeks to design and construct new biological parts, devices and systems, as well as to re-design existing components. However, rationally designed synthetic circuits may not work as expected due to the context-dependence of biological parts. Darwinian selection, the main mechanism through which evolution works, is a major force in creating biodiversity and may be a powerful tool for synthetic biology. This article reviews selection-based techniques and proposes strict Darwinian selection as an alternative approach for the identification and characterization of parts. Additionally, a strategy for fine-tuning of relatively complex circuits by coupling them to a master standard circuit is discussed

Analytic results for Gaussian wave packets in four model systems: I. Visualization of the kinetic energy

Using Gaussian wave packet solutions, we examine how the kinetic energy is distributed in time-dependent solutions of the Schrodinger equation corresponding to the cases of a free particle, a particle undergoing uniform acceleration, a particle in a harmonic oscillator potential, and a system corresponding to an unstable equilibrium. We find, for specific choices of initial parameters, that as much as 90% of the kinetic energy can be localized (at least conceptually) in the `front half' of such Gaussian wave packets, and we visualize these effects.Comment: 22 pages, RevTeX, four .eps figures, to appear in Found. Phys. Lett. Vol. 17, Dec. 200

Differential Myocardial Gene Delivery by Recombinant Serotype-Specific Adeno-associated Viral Vectors

AbstractRecombinant cross-packaging of adeno-associated virus (AAV) genome of one serotype into other AAV serotypes has the potential to optimize tissue-specific gene transduction and expression in the heart. To evaluate the role of AAV1 to 5 virion shells on AAV2 transgene transduction, we constructed hybrid vectors in which each serotype capsid coding domain was cloned into a common vector backbone containing AAV2 replication genes. Constructs were tested for expression in: (1) adult murine heart in vivo using direct injection of virus, (2) neonatal and adult murine ventricular cardiomyocytes in vitro, and (3) adult human ventricular cardiomyocytes in vitro, using green fluorescent protein (GFP) as the measurable transgene. Serotype 1 virus demonstrated the highest transduction efficiency in adult murine cardiomyocytes both in vitro and in vivo, while serotype 2 virus had the greater transduction efficiency in neonatal cardiomyocytes in vitro. Prolonged in vivo myocardial GFP expression was observed for up to 12 months using serotype 1 and 2 vectors only. In human cardiomyocytes, serotype 1 vector was superior in transduction efficiency, followed by types 2, 5, 4, and 3. These data establish a hierarchy for efficient serotype-specific vector transduction in myocardial tissue. AAV1 serotype packaging results in more efficient transduction of genes in the murine and human adult heart, compared to other AAV serotypes. Our results suggest that adult human cardiac gene therapy may be enhanced by the use of serotype 1-specific AAV vectors

Effects of signs in tunneling matrix elements on transmission zeros and phase

The effect of the signs in the tunneling matrix elements on the transmission zeros and the transmission phase in transport through a quantum dot is studied. The existence of the transmission zeros is determined by both the relative signs and the strength of the tunneling matrix elements for two neighboring energy levels of a dot. The experimentally observed oscillating behavior of the transmission phase over several Coulomb peaks can be explained by the uniform distribution of the relative signs. Based on the simple model of a quantum dot, we present a possible scenario which can give the uniform signs over several conductance peaks. We suggest that the location of the transmission zeros can be identified by inspecting the Fano interference pattern in the linear response conductance of the Aharonov-Bohm (AB) interferometer with an embedded quantum as a function of the number of electrons in a dot and the AB flux.Comment: 9 pages, 6 figures. Accepted for publication in Phys. Rev.

Prokayrotic Ubiquitin-Like Protein (Pup) Proteome of Mycobacterium tuberculosis

Prokaryotic ubiquitin-like protein (Pup) in Mycobacterium tuberculosis (Mtb) is the first known post-translational small protein modifier in prokaryotes, and targets several proteins for degradation by a bacterial proteasome in a manner akin to ubiquitin (Ub) mediated proteolysis in eukaryotes. To determine the extent of pupylation in Mtb, we used tandem affinity purification to identify its “pupylome”. Mass spectrometry identified 55 out of 604 purified proteins with confirmed pupylation sites. Forty-four proteins, including those with and without identified pupylation sites, were tested as substrates of proteolysis in Mtb. Under steady state conditions, the majority of the test proteins did not accumulate in degradation mutants, suggesting not all targets of pupylation are necessarily substrates of the proteasome under steady state conditions. Four proteins implicated in Mtb pathogenesis, Icl (isocitrate lyase), Ino1 (inositol-1-phosphate synthase), MtrA (Mtb response regulator A) and PhoP (phosphate response regulator P), showed altered levels in degradation defective Mtb. Icl, Ino1 and MtrA accumulated in Mtb degradation mutants, suggesting these proteins are targeted to the proteasome. Unexpectedly, PhoP was present in wild type Mtb but undetectable in the degradation mutants. Taken together, these data demonstrate that pupylation regulates numerous proteins in Mtb and may not always lead to degradation

phot1 inhibition of ABCB19 primes lateral auxin fluxes in the shoot apex required for phototropism

It is well accepted that lateral redistribution of the phytohormone auxin underlies the bending of plant organs towards light. In monocots, photoreception occurs at the shoot tip above the region of differential growth. Despite more than a century of research, it is still unresolved how light regulates auxin distribution and where this occurs in dicots. Here, we establish a system in Arabidopsis thaliana to study hypocotyl phototropism in the absence of developmental events associated with seedling photomorphogenesis. We show that auxin redistribution to the epidermal sites of action occurs at and above the hypocotyl apex, not at the elongation zone. Within this region, we identify the auxin efflux transporter ATP-BINDING CASSETTE B19 (ABCB19) as a substrate target for the photoreceptor kinase PHOTOTROPIN 1 (phot1). Heterologous expression and physiological analyses indicate that phosphorylation of ABCB19 by phot1 inhibits its efflux activity, thereby increasing auxin levels in and above the hypocotyl apex to halt vertical growth and prime lateral fluxes that are subsequently channeled to the elongation zone by PIN-FORMED 3 (PIN3). Together, these results provide new insights into the roles of ABCB19 and PIN3 in establishing phototropic curvatures and demonstrate that the proximity of light perception and differential phototropic growth is conserved in angiosperm