306 research outputs found
Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules.
A detailed study of energy differences between the highest occupied and
lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and
water clusters is presented. Recent work questioning the applicability of
Kohn-Sham density-functional theory to proteins and large water clusters (E.
Rudberg, J. Phys.: Condens. Mat. 2012, 24, 072202) has demonstrated vanishing
HOMO-LUMO gaps for these systems, which is generally attributed to the
treatment of exchange in the functional used. The present work shows that the
vanishing gap is, in fact, an electrostatic artefact of the method used to
prepare the system. Practical solutions for ensuring the gap is maintained when
the system size is increased are demonstrated. This work has important
implications for the use of large-scale density-functional theory in
biomolecular systems, particularly in the simulation of photoemission, optical
absorption and electronic transport, all of which depend critically on
differences between energies of molecular orbitals.Comment: 13 pages, 4 figure
Diffusion in the special theory of relativity
The Markovian diffusion theory is generalized within the framework of the
special theory of relativity using a modification of the mathematical calculus
of diffusion on Riemannian manifolds (with definite metric) to describe
diffusion on Lorentzian manifolds with an indefinite metric. A generalized
Langevin equation in the fiber space of position, velocity and orthonormal
velocity frames is defined from which the generalized relativistic Kramers
equation in the phase space in external force fields is derived. The obtained
diffusion equation is invariant under Lorentz transformations and its
stationary solution is given by the J\"{u}ttner distribution. Besides a
non-stationary analytical solution is derived for the example of force-free
relativistic diffusion.Comment: 10 pages, 1 figur
O(N) methods in electronic structure calculations
Linear scaling methods, or O(N) methods, have computational and memory
requirements which scale linearly with the number of atoms in the system, N, in
contrast to standard approaches which scale with the cube of the number of
atoms. These methods, which rely on the short-ranged nature of electronic
structure, will allow accurate, ab initio simulations of systems of
unprecedented size. The theory behind the locality of electronic structure is
described and related to physical properties of systems to be modelled, along
with a survey of recent developments in real-space methods which are important
for efficient use of high performance computers. The linear scaling methods
proposed to date can be divided into seven different areas, and the
applicability, efficiency and advantages of the methods proposed in these areas
is then discussed. The applications of linear scaling methods, as well as the
implementations available as computer programs, are considered. Finally, the
prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys
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Purification and functional characterisation of rhiminopeptidase A, a novel aminopeptidase from the venom of Bitis gabonica rhinoceros
This study describes the discovery and characterisation of a novel aminopeptidase A from the venom of B. g. rhinoceros and highlights its potential biological importance. Similar to mammalian aminopeptidases, rhiminopeptidase A might be capable of playing roles in altering the blood pressure and brain function of victims. Furthermore, it could have additional effects on the biological functions of other host proteins by cleaving their N-terminal amino acids. This study points towards the importance of complete analysis of individual components of snake venom in order to develop effective therapies for snake bites
Towards Graphene Nanoribbon-based Electronics
The successful fabrication of single layer graphene has greatly stimulated
the progress of the research on graphene. In this article, focusing on the
basic electronic and transport properties of graphene nanoribbons (GNRs), we
review the recent progress of experimental fabrication of GNRs, and the
theoretical and experimental investigations of physical properties and device
applications of GNRs. We also briefly discuss the research efforts on the spin
polarization of GNRs in relation to the edge states.Comment: 9pages,10figure
Properties of Graphene: A Theoretical Perspective
In this review, we provide an in-depth description of the physics of
monolayer and bilayer graphene from a theorist's perspective. We discuss the
physical properties of graphene in an external magnetic field, reflecting the
chiral nature of the quasiparticles near the Dirac point with a Landau level at
zero energy. We address the unique integer quantum Hall effects, the role of
electron correlations, and the recent observation of the fractional quantum
Hall effect in the monolayer graphene. The quantum Hall effect in bilayer
graphene is fundamentally different from that of a monolayer, reflecting the
unique band structure of this system. The theory of transport in the absence of
an external magnetic field is discussed in detail, along with the role of
disorder studied in various theoretical models. We highlight the differences
and similarities between monolayer and bilayer graphene, and focus on
thermodynamic properties such as the compressibility, the plasmon spectra, the
weak localization correction, quantum Hall effect, and optical properties.
Confinement of electrons in graphene is nontrivial due to Klein tunneling. We
review various theoretical and experimental studies of quantum confined
structures made from graphene. The band structure of graphene nanoribbons and
the role of the sublattice symmetry, edge geometry and the size of the
nanoribbon on the electronic and magnetic properties are very active areas of
research, and a detailed review of these topics is presented. Also, the effects
of substrate interactions, adsorbed atoms, lattice defects and doping on the
band structure of finite-sized graphene systems are discussed. We also include
a brief description of graphane -- gapped material obtained from graphene by
attaching hydrogen atoms to each carbon atom in the lattice.Comment: 189 pages. submitted in Advances in Physic
Development of cognitive enhancers based on inhibition of insulin-regulated aminopeptidase
The peptides angiotensin IV and LVV-hemorphin 7 were found to enhance memory in a number of memory tasks and reverse the performance deficits in animals with experimentally induced memory loss. These peptides bound specifically to the enzyme insulin-regulated aminopeptidase (IRAP), which is proposed to be the site in the brain that mediates the memory effects of these peptides. However, the mechanism of action is still unknown but may involve inhibition of the aminopeptidase activity of IRAP, since both angiotensin IV and LVV-hemorphin 7 are competitive inhibitors of the enzyme. IRAP also has another functional domain that is thought to regulate the trafficking of the insulin-responsive glucose transporter GLUT4, thereby influencing glucose uptake into cells. Although the exact mechanism by which the peptides enhance memory is yet to be elucidated, IRAP still represents a promising target for the development of a new class of cognitive enhancing agents
Gender-specific associations of vision and hearing impairments with adverse health outcomes in older Japanese: a population-based cohort study
BACKGROUND: Several epidemiological studies have shown that self-reported vision and hearing impairments are associated with adverse health outcomes (AHOs) in older populations; however, few studies have used objective sensory measurements or investigated the role of gender in this association. Therefore, we examined the association of vision and hearing impairments (as measured by objective methods) with AHOs (dependence in activities of daily living or death), and whether this association differed by gender. METHODS: From 2005 to 2006, a total of 801 residents (337 men and 464 women) aged 65 years or older of Kurabuchi Town, Gunma, Japan, participated in a baseline examination that included vision and hearing assessments; they were followed up through September 2008. Vision impairment was defined as a corrected visual acuity of worse than 0.5 (logMAR = 0.3) in the better eye, and hearing impairment was defined as a failure to hear a 30 dB hearing level signal at 1 kHz in the better ear. Information on outcomes was obtained from the town hall and through face-to-face home visit interviews. We calculated the risk ratios (RRs) of AHOs for vision and hearing impairments according to gender. RESULTS: During a mean follow-up period of 3 years, 34 men (10.1%) and 52 women (11.3%) had AHOs. In both genders, vision impairment was related to an elevated risk of AHOs (multi-adjusted RR for men and women together = 1.60, 95% CI = 1.05-2.44), with no statistically significant interaction between the genders. In contrast, a significant association between hearing impairment and AHOs (multi-adjusted RR = 3.10, 95% CI = 1.43-6.72) was found only in the men. CONCLUSION: In this older Japanese population, sensory impairments were clearly associated with AHOs, and the association appeared to vary according to gender. Gender-specific associations between sensory impairments and AHOs warrant further investigation
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