ncRNA-mediated bistability in the synthesis of hundreds of distinct mRNAs and proteins

The kinetics of gene expression can be bistable due to the feedback between the mRNA and protein formation. In eukaryotic cells, the interplay between mRNAs and proteins can be influenced by non-coding RNAs. Some of these RNAs, e.g., microRNAs, may target hundreds of distinct mRNAs. The model presented here shows how a non-coding RNA can be used as a mediator in order to involve numerous mRNAs and proteins into a bistable network.     

Coupling Effect of Ion Channel Clusters on Calcium Signalling

Based on a modified intracellular Ca^2＋ model involving diffusive coupling of two calcium ion channel dusters, the effects of coupling on calcium signalling are numerically investigated. The simulation results indicate that the diffusive coupling of dusters together with internal noise determine the calcium dynamics of single duster, and for either homogeneous or heterogeneous coupled dusters, the synchronization of dusters, which is important to calcium signalling, is enhanced by the coupling effect.     

The conductance of SnO2 small nanowires: A study based on density functional and scattering theories

This study is motivated by the recent advances in the fabrication of oxide nanostructures and its purpose is the assessment of the relationship between their structural properties and the conductance. The structures considered are small SnO₂ nanowires whose size and shape reproduce on a smaller scale the structures produced by current technologies. Their electronic configuration and the conductance are evaluated using the density functional and scattering theories with a simplified modelling of the external leads. The study of the electronic configuration shows that the structure of the allowed energy levels and of the charges responds to the details of the nanowire structure and composition. These effects are important in the context of the conductance. In fact, deep resonances are produced by the alignment of the allowed energy levels in the nanowire with the ones in the external leads. For these conductive channels the relationship between the size and the conductance parallels the one between the size and the binding energy.     

Calculations of Optical Rotation from Density Functional Theory

Density function theory calculations of frequency-dependent optical rotations [α]ω for three rigid chiral molecules are reported. Calculations have been carried out at the sodium D line frequency, using the ADZP basis set and a wide variety of functionals. Gauge-invariant atomic orbitals are used to guarantee origin-independent values of [ω]D. In addition, study of geometry dependence of [ω]D is reported. Using the geometries optimized at the B3LYP/ADZP level, the mean absolute deviation of B3LYP/ADZP and experimental laiD values yields 60.1°/（dm g/cm^3）. According to our knowledge, this value has not been achieved until now with any other model.     

Global analysis of the immune response

The immune system may be seen as a complex system, characterized using tools developed in the study of such systems, for example, surface roughness and its associated Hurst exponent. We analyze densitometric (Panama blot) profiles of immune reactivity, to classify individuals into groups with similar roughness statistics. We focus on a population of individuals living in a region in which malaria endemic, as well as a control group from a disease-free region. Our analysis groups individuals according to the presence, or absence, of malaria symptoms and number of malaria manifestations. Applied to the Panama blot data, our method proves more effective at discriminating between groups than principal-components analysis or super-paramagnetic clustering. Our findings provide evidence that some phenomena observed in the immune system can be only understood from a global point of view. We observe similar tendencies between experimental immune profiles and those of artificial profiles, obtained from an immune network model. The statistical entropy of the experimental profiles is found to exhibit variations similar to those observed in the Hurst exponent.     

Collectivity in the optical response. of small metal clusters

The question of whether the linear absorption spectra of metal clusters can be interpreted as density oscillations (collective “plasmons”) or can only be understood as transitions between distinct molecular states is still a matter of debate for clusters with only a few electrons. We calculate the photo-absorption spectra of Na₂ and Na₅ ⁺ comparing two different methods: quantum fluid dynamics and time-dependent density functional theory. The changes in the electronic structure associated with particular excitations are visualized in “snapshots” via transition densities. Our analysis shows that even for the smallest clusters, the observed excitations can be interpreted as intuitively understandable density oscillations. For Na₅ ⁺, the importance of self-interaction corrections to the adiabatic local density approximation is demonstrated. Received: 1 July 2001 / Published online: 10 October 2001     

Dependence on dilution of critical and compensation temperatures of a two-dimensional mixed spin-1/2 and spin-1 system

In this study, dependence on site dilution of critical and compensation temperatures of a two-dimensional mixed spin-1/2 and spin-1 system has been investigated with Monte Carlo simulation. The dependence of the thermal and magnetic behaviors on dilution of mixed spin system has been discussed. We have shown that the critical and compensation temperatures of diluted mixed spin system linearly decrease with increasing number of diluted sites.     

High resolution microwave spectroscopy of the isomeric pair vinylcyanoacetylene and cyanovinylacetylene

The carbon chain molecules vinylcyanoacetylene and cyanovinylacetylene have been investigated between 8 and 41 GHz by Fourier transform microwave spectroscopy of a supersonic molecular beam. Owing to the high spectral resolution of the present technique, significantly more accurate rotational and centrifugal distortion constants have been derived for both molecules. In addition, the dipole moments have been calculated at the B3LYP/cc-pVTZ level of theory. Because these carbon chains are similar in structure and composition to known astronomical molecules and because of their high polarity, both species are good candidates for radioastronomical detection.     

First-Principles Calculations for Structures and Melting Temperature of Si6 Clusters

We investigate the structures and the melting temperature of the Si6 cluster by using the first-principles pseudopotential method in real space and Langevin molecular dynamics. It is shown that the ground structure of the Si6 cluster is a square bipyramid, and the corresponding melting temperature is about 1923 K. In the heating procedure, the structures of the Si6 cluster change from high symmetry structures containing 5-8 bonds, via prolate structures containing 3-4 bonds, to oblate structures containing 1-2 bonds.     

Correlation in the velocity of a Brownian particle induced by frictional anisotropy and magnetic field

We study the motion of charged Brownian particles in an external magnetic field. It is found that a correlation appears between the components of particle velocity in the case of anisotropic friction, approaching asymptotically zero in the stationary limit. If magnetic field is smaller compared to the critical value, determined by frictional anisotropy, the relaxation of the correlation is non-oscillating in time. However, in a larger magnetic field this relaxation becomes oscillating. The phenomenon is related to the statistical dependence of the components of transformed random force caused by the simultaneous influence of magnetic field and anisotropic dissipation.     

Accumulating particles at the boundaries of a laminar flow

The accumulation of small particles is analyzed in stationary flows through channels of variable width at small Reynolds number. The combined influence of pressure, viscous drag and thermal fluctuations is described by means of a Fokker-Planck equation for the particle density. It is shown that for extended spherical particles the shape of the fluid domain gives rise to inhomogeneous particle densities, thereby leading to particle accumulation and corresponding depletion. For extended spherical particles, conditions are specified that lead to inhomogeneous densities and consequently to regions with particle accumulation and depletion.     

Analysis of heartbeat asymmetry based on multi-scale time irreversibility test

We investigate the asymmetry of heart rate control system and suggest a simple index to quantify this asymmetry by performing high-dimensional time irreversibility tests to heartbeat interval time series over multiple scales. The results provide strong evidence to the concept that the asymmetry is an intrinsic property of heart rate control system. As a simple and visual method, it is proved to be effective in classifying physiologic and synthetic subjects while the maximum scale is selected within a proper range, and also provides a new way to analyze the time irreversibility for other high-dimensional systems.     

A kinetic model for the premelting of a crystalline structure

An analytical kinetic approach to examine the premelting phenomenon is suggested by using a first passage time analysis. Premelting is considered to occur when the time of formation of a Frenkel type defect in the surface monolayer becomes sufficiently small. The mean time of defect formation on the surface lattice, i.e., the mean time necessary for a selected (surface-located) molecule to leave its lattice site and form a Frenkel defect, is calculated by using a first passage time analysis. The model is illustrated by numerical calculations for a crystalline structure composed of molecules interacting via the Lennard-Jones (LJ) potential. The lattice vectors in the plane parallel to the free surface of the crystal were assumed to be equal (to the lattice parameter) and the angle between them was varied. The model predictions of the Tammann temperature (of premelting) are very sensitive to the parameters of the LJ potential. In all the cases considered, the temperature dependence of the mean first passage time has two clearly distinct regimes: at low temperatures the dependence is sharp and at high temperatures it is weak.     

Density functional theory study of the electronic and field emission properties of nitrogen- and boron-doped carbon nanocones

Using first-principles density functional theory, we have investigated the electronic and field emission properties of carbon nanocones (CNCs) doped with N or B with 60° disclination. Our findings are that the emission properties for the doped CNCs depend on the doping species, position, and concentration. Compared to pristine CNC, N-doped CNCs exhibit better field emission properties, in which as the doping concentration increases from 1.25% to 2.5% the maximum emission current at applied electric field of 0.3 V/Å increases from 0.94 μA (one N atom is doped at the position adjacent to the pentagon) to 2.90 μA (two N atoms are doped at pentagon). As for pristine CNC the emission current is only 0.21 μA. However, B-doping has no significant influence on the emission properties of CNCs. Our findings suggest that N-doped CNCs can be used as a candidate for cold-emission electron sources.     

Electronic structure of Li3GaN2

First principles calculations, by means of the full-potential linearized augmented plane wave method within the local density approximation, were carried out for the electronic properties of Li₃GaN₂. The calculated lattice parameter is in good agreement with the measured one. The bandgap is direct at the Brillouin zone centre. The Li-N and Ga-N bonds are both ionic with a small covalent character of the latter one.     

First-principles study of arsenic impurity clusters in molecular beam epitaxy (MBE) grown HgCdTe

The understanding of the microstructures of the arsenic tetramer , dimer , and singlet of HgCdTe is important to explain the high electrical compensation of molecular beam epitaxy (MBE) samples and the conversion to p-type behavior. The stable configurations were obtained from the first-principles calculations for the arsenic cluster defects [ (n=1, 2, and 4)] in as-grown HgCdTe. According to the defect formation energies calculated under Te-rich conditions, the most probable configurations of , , and have been established. For the optimized and the energy is favorable to combine in a nearest neighboring mercury vacancy , and the corresponding configurations can be used to explain the self-compensated n-type characteristics in as-grown materials. is likely to be more abundant than in as-grown materials, but arsenic atoms are more strongly bounded in than in , thus more substantial activation energy is needed for than that for . The atomic relaxations as well as the structural stability of the arsenic defects have also been investigated.     

A long-range memory stochastic model of the return in financial markets

We present a nonlinear stochastic differential equation (SDE) which mimics the probability density function (PDF) of the return and the power spectrum of the absolute return in financial markets. Absolute return as a measure of market volatility is considered in the proposed model as a long-range memory stochastic variable. The SDE is obtained from the analogy with an earlier proposed model of trading activity in the financial markets and generalized within the nonextensive statistical mechanics framework. The proposed stochastic model generates time series of the return with two power law statistics, i.e., the PDF and the power spectral density, reproducing the empirical data for the one-minute trading return in the NYSE.     

Stability and Growth Modes of Ni--C Clusters: A Study based on All-Electron Density Function Theory

Growth modes of the free-standing NiCN （N ≤ 8） and Ni2CN （N ≤ 8） dusters are investigated by the allelectron density functional theory. The results reveal that there are two competing modes for the growth of these clusters： the linear chain and the ring structure without transannular bonds. The lowest-energy geometries of NiCN （N ≤ 8） are the linear chains with the Ni atom at one end, except for NiC2 and NiCT. The Ni2CN （N ≤ 8） clusters all prefer to the linear chains with the two Ni atoms at the two ends. Miilliken population analysis indicates that the total spin of the lowest-energy cluster show significant odd-even alternation. The NiMCN （M = 1,2） clusters with the even N are one and those with the odd-N are zero.     

Simulations of flexible membranes using a coarse-grained particle-based model with spontaneous curvature variables

We propose a simple mathematical model for lipid bilayer membranes of flexible fluid or solid state. The model consists of interacting coarse-grained particles with two extra variables. One indicates the spontaneous curvature at the particle position, and the other indicates the vector representing the direction normal to the membrane. When the spontaneous curvature variable is allowed to fluctuate significantly, the fluctuation causes a softening of the membrane and growth of large undulations as the amplitude of the fluctuation is increased. By changing the amplitude of the fluctuation in simulations, the bending rigidity of the membrane can be easily controlled. Because the proposed model includes anisotropic interactions between the particles, multilayered vesicles can be obtained through a reversible transition by weakening the strength of the anisotropic interactions.