Simulation of RNA silencing pathway for time-dependent transgene transcription rate

The synthesis of dsRNA is analyzed using a pathway model with amplifications caused by the aberrant RNAs. The transgene influx rate is assumed time-decaying considering the fact that the number of transgenes can not be infinite. The dynamics of the transgene induced RNA silencing is investigated using a system of coupled nonautonomous ordinary nonlinear differential equations which describe the model phenomenologically. The silencing phenomena are detected after a period of transcription. Important contributions of certain parameters are discussed with several numerical examples.

Time-dependent transitions with time-space noncommutativity and its implications in quantum optics

We study the time-dependent transitions of a quantum-forced harmonic oscillator in noncommutative R(1,1) perturbatively to linear order in the noncommutativity theta. We show that the Poisson distribution gets modified, and that the vacuum state evolves into a `squeezed' state rather than a coherent state. The time evolutions of uncertainties in position and momentum in vacuum are also studied and imply interesting consequences for modeling nonlinear phenomena in quantum optics.

Effect of dimerization on dynamics of spin-charge separation in Pariser-Parr-Pople model: A time-dependent density matrix renormalization group study

We investigate the effect of static electron-phonon coupling on real-time dynamics of spin and charge transport in pi-conjugated polyene chains. The polyene chain is modeled by the Pariser-Parr-Pople Hamiltonian with dimerized nearest-neighbor parameter t(0)(1 + delta) for short bonds and t(0)(1 - delta) for long bonds, and long-range electron-electron interactions. We follow the time evolution of the spin and charge using time-dependent density matrix renormalization group technique when a hole is injected at one end of the chain in its ground state. We find that spin and charge dynamics followed through spin and charge velocities depend both on chain length and extent of dimerization delta. Analysis of the results requires focusing on physical quantities such as average spin and charge polarizations, particularly in the large dimerization limit. In the dimerization range 0.0 <= delta <= 0.15, spin-charge dynamics is found to have a well-defined behavior, with spin-charge separation (measured as the ratio of charge velocity to spin velocity) as well as the total amount of charge and spin transported in a given time along the chain decreasing as dimerization increases. However, in the range 0.3 <= delta <= 0.5, it is observed that the dynamics of spin and charge transport becomes complicated. It is observed that, for large delta values, spin-charge separation is suppressed and the injected hole fails to travel the entire length of the chain.

Time-Dependent Predominance of Nonhomologous DNA End-Joining Pathways during Embryonic Development in Mice

Repair of DNA double-strand breaks (DSBs) is crucial for maintaining genomic integrity during the successful development of a fertilized egg into a whole organism. To date, the mechanism of DSB repair in postimplantation embryos has been largely unknown. In the present study, using a cell-free repair system derived from the different embryonic stages of mice, we find that canonical nonhomologous end joining (NHEJ), one of the major DSB repair pathways in mammals, is predominant at 14.5 day of embryonic development. Interestingly, all four types of DSBs tested were repaired by ligase IV/XRCC4 and Ku-dependent classical NHEJ. Characterization of end-joined junctions and expression studies further showed evidences for canonical NHEJ. Strikingly, in contrast to the above, we observed noncanonical end joining accompanied by DSB resection, dependent on microhomology and ligase III in 18.5-day embryos. Interestingly, we observed an elevated expression of CtIP, MRE11, and NBS1 at this stage, suggesting that it could act as a switch between classical end joining and microhomology-mediated end joining at later stages of embryonic development. Thus, our results establish for the first time the existence of both canonical and alternative NHEJ pathways during the postimplantation stages of mammalian embryonic development. (C) 2012 Elsevier Ltd. All rights reserved.

Increased time-dependent room temperature plasticity in metallic glass nanopillars and its size-dependency

Room temperature, uniaxial compression creep experiments were performed on micro-/nano-sized pillars (having diameters in the range of 250-2000 nm) of a Zr-based bulk metallic glass (BMG) to investigate the influence of sample size on the time-dependent plastic deformation behavior in amorphous alloys. Experimental results reveal that plastic deformation indeed occurs at ambient temperature and at stresses that are well below the nominal quasi-static yield stress. At a given stress, higher total strains accrue in the smaller specimens. In all cases, plastic deformation was found to be devoid of shear bands, i.e., it occurs in homogeneous manner. The stress exponent obtained from the slope of the linear relation between strain rate and applied stress also shows a strong size effect, which is rationalized in terms of the amount of free volume created during deformation and the surface-to-volume ratio of the pillar. (C) 2012 Elsevier Ltd. All rights reserved.

Optimal control problem for the time-dependent Kirchhoff-Love plate in a domain with rough boundary

In this paper, we study the asymptotic behavior of an optimal control problem for the time-dependent Kirchhoff-Love plate whose middle surface has a very rough boundary. We identify the limit problem which is an optimal control problem for the limit equation with a different cost functional.

Time dependent superhydrophobicity of drag reducing surfaces

Air can be trapped on the crevices of specially textured hydrophobic surfaces immersed in water. This heterogenous state of wetting in which the water is in contact with both the solid surface and the entrapped air is not stable. Diffusion of air into the surrounding water leads to gradual reduction in the size and numbers of the air bubbles. The sustainability of the entrapped air on such surfaces is important for many underwater applications in which the surfaces have to remain submersed for longer time periods. In this paper we explore the suitability of different classes of surface textures towards the drag reduction application by evaluating the time required for the disappearance of the air bubbles under hydrostatic conditions. Different repetitive textures consisting of holes, pillars and ridges of different sizes have been generated in silicon, aluminium and brass by isotropic etching, wire EDM and chemical etching respectively. These surfaces were rendered hydrophobic with self-assembled layer of fluorooctyl trichlorosilane for silicon and aluminium surfaces and 1-dodecanethiol for brass surfaces. Using total internal reflection the air bubbles are visualized with the help of a microscope and time lapse photography. Irrespective of the texture, both the size and the number of air pockets were found to decrease with time gradually and eventually disappear. In an attempt to reverse the diffusion we explore the possibility of using electrolysis to generate gases at the textured surfaces. The gas bubbles are nucleated everywhere on the surface and as they grow they coalesce with each other and get pinned at the texture edges.

Solution of Time Dependent Joule Heat Equation for a Graphene Sheet Under Thomson Effect

We address a physics-based solution of joule heating phenomenon in a single-layer graphene (SLG) sheet under the presence of Thomson effect. We demonstrate that the temperature in an isotopically pure (containing only C-12) SLG sheet attains its saturation level quicker than when doped with its isotopes (C-13). From the solution of the joule heating equation, we find that the thermal time constant of the SLG sheet is in the order of tenths of a nanosecond for SLG dimensions of a few micrometers. These results have been formulated using the electron interactions with the inplane and flexural phonons to demonstrate a field-dependent Landauer transmission coefficient. We further develop an analytical model of the SLG specific heat using the quadratic (out of plane) phonon band structure over the room temperature. Additionally, we show that a cooling effect in the SLG sheet can be substantially enhanced with the addition of C-13. The methodologies as discussed in this paper can be put forward to analyze the graphene heat spreader theory.

Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics

A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times-the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies. (c) 2015 AIP Publishing LLC.

THREE-LAYER FLUID FLOW OVER A SMALL OBSTRUCTION ON THE BOTTOM OF A CHANNEL

Many boundary value problems occur in a natural way while studying fluid flow problems in a channel. The solutions of two such boundary value problems are obtained and analysed in the context of flow problems involving three layers of fluids of different constant densities in a channel, associated with an impermeable bottom that has a small undulation. The top surface of the channel is either bounded by a rigid lid or free to the atmosphere. The fluid in each layer is assumed to be inviscid and incompressible, and the flow is irrotational and two-dimensional. Only waves that are stationary with respect to the bottom profile are considered in this paper. The effect of surface tension is neglected. In the process of obtaining solutions for both the problems, regular perturbation analysis along with a Fourier transform technique is employed to derive the first-order corrections of some important physical quantities. Two types of bottom topography, such as concave and convex, are considered to derive the profiles of the interfaces. We observe that the profiles are oscillatory in nature, representing waves of variable amplitude with distinct wave numbers propagating downstream and with no wave upstream. The observations are presented in tabular and graphical forms.

Phase space path integral approach to harmonic oscillator with a time-dependent force constant

The quantum statistical mechanical propagator for a harmonic oscillator with a time-dependent force constant, m omega(2)(t), has been investigated in the past and was found to have only a formal solution in terms of the solutions of certain ordinary differential equations. Such path integrals are frequently encountered in semiclassical path integral evaluations and having exact analytical expressions for such path integrals is of great interest. In a previous work, we had obtained the exact propagator for motion in an arbitrary time-dependent harmonic potential in the overdamped limit of friction using phase space path integrals in the context of Levy flights - a result that can be easily extended to Brownian motion. In this paper, we make a connection between the overdamped Brownian motion and the imaginary time propagator of quantum mechanics and thereby get yet another way to evaluate the latter exactly. We find that explicit analytic solution for the quantum statistical mechanical propagator can be written when the time-dependent force constant has the form omega(2)(t) = lambda(2)(t) - d lambda(t)/dt where lambda(t) is any arbitrary function of t and use it to evaluate path integrals which have not been evaluated previously. We also employ this method to arrive at a formal solution of the propagator for both Levy flights and Brownian subjected to a time-dependent harmonic potential in the underdamped limit of friction. (C) 2015 Elsevier B.V. All rights reserved.

Solid-state optical absorption from optimally tuned time-dependent range-separated hybrid density functional theory

We present a framework for obtaining reliable solid-state charge and optical excitations and spectra from optimally tuned range-separated hybrid density functional theory. The approach, which is fully couched within the formal framework of generalized Kohn-Sham theory, allows for the accurate prediction of exciton binding energies. We demonstrate our approach through first principles calculations of one- and two-particle excitations in pentacene, a molecular semiconducting crystal, where our work is in excellent agreement with experiments and prior computations. We further show that with one adjustable parameter, set to produce the known band gap, this method accurately predicts band structures and optical spectra of silicon and lithium fluoride, prototypical covalent and ionic solids. Our findings indicate that for a broad range of extended bulk systems, this method may provide a computationally inexpensive alternative to many-body perturbation theory, opening the door to studies of materials of increasing size and complexity.

Time-dependent nanoscale plasticity in nanocrystalline nickel rods and tubes

Time-dependent nanoscale plasticity of nanocrystalline nickel at room temperature was critically explored through a series of micropillar creep and quasi-static compression experiments on rod and tube specimens fabricated by electron beam lithography and electroplating. Enhanced creep rates in tubes as compared to rods, establishes the facilitating role played by the free surface in time-dependent deformation. Creep stress exponent, n, and strain-rate sensitivity, m, were compared to examine connections between creep and the rate-dependent plasticity, if any. (C) 2015 Elsevier Ltd. All rights reserved.

Triplet excited electronic state switching induced by hydrogen bonding: A transient absorption spectroscopy and time-dependent DFT study

The solvent plays a decisive role in the photochemistry and photophysics of aromatic ketones. Xanthone (XT) is one such aromatic ketone and its triplet-triplet (T-T) absorption spectra show intriguing solvatochromic behavior. Also, the reactivity of XT towards H-atom abstraction shows an unprecedented decrease in protic solvents relative to aprotic solvents. Therefore, a comprehensive solvatochromic analysis of the triplet-triplet absorption spectra of XT was carried out in conjunction with time dependent density functional theory using the ad hoc explicit solvent model approach. A detailed solvatochromic analysis of the T-T absorption bands of XT suggests that the hydrogen bonding interactions are different in the corresponding triplet excited states. Furthermore, the contributions of non-specific and hydrogen bonding interactions towards differential solvation of the triplet states in protic solvents were found to be of equal magnitude. The frontier molecular orbital and electron density difference analysis of the T-1 and T-2 states of XT indicates that the charge redistribution in these states leads to intermolecular hydrogen bond strengthening and weakening, respectively, relative to the S-0 state. This is further supported by the vertical excitation energy calculations of the XT-methanol supra-molecular complex. The intermolecular hydrogen bonding potential energy curves obtained for this complex in the S-0, T-1, and T-2 states support the model. In summary, we propose that the different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states of XT result in a decreasing role of the n pi* triplet state, and are thus responsible for its reduced reactivity towards H-atom abstraction in protic solvents. (C) 2016 AIP Publishing LLC.