Interplay between multiple length and time scales in complex chemical systems

Processes in complex chemical systems, such as macromolecules, electrolytes, interfaces, micelles and enzymes, can span several orders of magnitude in length and time scales. The length and time scales of processes occurring over this broad time and space window are frequently coupled to give rise to the control necessary to ensure specificity and the uniqueness of the chemical phenomena. A combination of experimental, theoretical and computational techniques that can address a multiplicity of length and time scales is required in order to understand and predict structure and dynamics in such complex systems. This review highlights recent experimental developments that allow one to probe structure and dynamics at increasingly smaller length and time scales. The key theoretical approaches and computational strategies for integrating information across time-scales are discussed. The application of these ideas to understand phenomena in various areas, ranging from materials science to biology, is illustrated in the context of current developments in the areas of liquids and solvation, protein folding and aggregation and phase transitions, nucleation and self-assembly.

Turvemaan männyn (Pinus sylvestris L.) ja kuusen (Picea abies [L.] Karst.) kanto- ja juuripuun ominaisuudet ja asetoniliukoisten uuteaineiden määrä

Tutkimus on osa Metsäklusteri Oy:n Future Biorefinery –tutkimusohjelmaa, jossa kartoitetaan mahdollisuuksia hyödyntää metsäteollisuuden raaka-aineita aiempaa tarkemmin ja uusissa tuotteissa. Tutkimuksen tavoitteena on selvittää männyn (Pinus sylvestris L.) ja kuusen (Picea abies [L.] Karst.) juurten ja kantopuun rakenne ja ominaisuudet. Tutkimuksessa selvitetään löytyykö männyn ja kuusen juurista reaktiopuuta ja määritetään asetoniliukoisten uuteaineiden osuus kantoja juuripuussa. Tutkimusaineistona oli viisi eri-ikäistä mäntyä ja viisi eri-ikäistä kuusta. Juuri- ja kantoaineisto kerättiin Metsäntutkimuslaitoksen toimesta Parkanon seudulta (62.017°N, 23.017°E) hakkuun jälkeen. Maanalaisista juurista otettiin näytteet kolmelta eri etäisyydeltä juurenniskaan nähden. Kummankaan lajin juurista ei löytynyt varsinaista reaktiopuuta, mutta joissakin näytteissä havaittiin lievää reaktiopuuta. Lievää reaktiopuuta löytyi enemmän männyn kuin kuusen juurista, eikä sitä löytynyt lainkaan kaikkein ohuimmista, noin 2 cm paksuisista juurenosista. Männyn kannoissa uuteaineprosentti oli korkeampi kuin kuusen. Männyn juurissa uuteaineprosentti kasvoi edettäessä kohti juuren kärkeä. Kuusella uuteaineprosentti laski aluksi, mutta lähellä juuren kärkeä taas kasvoi. Kuoren uuteainepitoisuus oli molemmilla puulajeilla korkeampi kuin puuaineen. Tutkimusaineisto oli suppea, eikä tutkimuksessa pyritty tilastolliseen yleistettävyyteen. Laajemmasta aineistosta tehdylle tutkimukselle on tarvetta, sillä turvekankailta saatavan puun tarjonta on Suomessa kasvussa, mutta juurten uuteaine- ja reaktiopuututkimuksia on tehty vain kivennäismailta kerätyistä aineistoista.

A kinetic Ising model study of dynamical correlations in confined fluids: Emergence of both fast and slow time scales

Experiments and computer simulation studies have revealed existence of rich dynamics in the orientational relaxation of molecules in confined systems such as water in reverse micelles, cyclodextrin cavities, and nanotubes. Here we introduce a novel finite length one dimensional Ising model to investigate the propagation and the annihilation of dynamical correlations in finite systems and to understand the intriguing shortening of the orientational relaxation time that has been reported for small sized reverse micelles. In our finite sized model, the two spins at the two end cells are oriented in the opposite directions to mimic the effects of surface that in real system fixes water orientation in the opposite directions. This produces opposite polarizations to propagate inside from the surface and to produce bulklike condition at the center. This model can be solved analytically for short chains. For long chains, we solve the model numerically with Glauber spin flip dynamics (and also with Metropolis single-spin flip Monte Carlo algorithm). We show that model nicely reproduces many of the features observed in experiments. Due to the destructive interference among correlations that propagate from the surface to the core, one of the rotational relaxation time components decays faster than the bulk. In general, the relaxation of spins is nonexponential due to the interplay between various interactions. In the limit of strong coupling between the spins or in the limit of low temperature, the nature of relaxation of the spins undergoes a qualitative change with the emergence of a homogeneous dynamics where decay is predominantly exponential, again in agreement with experiments. (C) 2010 American Institute of Physics. doi: 10.1063/1.3474948]

Climatic adaptation of Norway spruce (Picea abies (L.) Karsten) in Finland based on male flowering phenology.

Anthesis was studied at the canopy level in 10 Norway spruce stands from 9 localities in Finland from 1963 to 1974. Distributions of pollen catches were compared to the normal Gaussian distribution. The basis for the timing studies was the 50 per cent point of the anthesis-fitted normal distribution. Development up to this point was given in calendar days, in degree days (>5 °C) and in period units. The count of each parameter began on March 19 (included). Male flowering in Norway spruce stands was found to have more annual variation in quantity than in Scots pine stands studied earlier. Anthesis in spruce in northern Finland occurred at a later date than in the south. The heat sums needed for anthesis varied latitudinally less in spruce than in pine. The variation of pollen catches in spruce increased towards north-west as in the case of Scots pine. In the unprocessed data, calendar days were found to be the most accurate forecast of anthesis in Norway spruce both for a single year and for the majority of cases of stand averages over several years. Locally, the period unit could be a more accurate parameter for the stand average. However, on a calendar day basis, when annual deviations between expected and measured heat sums were converted to days, period units were narrowly superior to days. The geographical correlations respect to timing of flowering, calculated against distances measured along simulated post-glacial migration routes, were stronger than purely latitudinal correlations. Effects of the reinvasion of Norway spruce into Finland are thus still visible in spruce populations just as they were in Scots pine populations. The proportion of the average annual heat sum needed for spruce anthesis grew rapidly north of a latitude of ca. 63° and the heat sum needed for anthesis decreased only slighty towards the timberline. In light of flowering phenology, it seems probable that the northwesterly third of Finnish Norway spruce populations are incompletely adapted to the prevailing cold climate. A moderate warming of the climate would therefore be beneficial for Norway spruce. This accords roughly with the adaptive situation in Scots pine.

Resistance of Norway spruce (Picea abies) to root and butt rot (Heterobasidion parviporum) in peatland and mineral soil

Root and butt rot is the most harmful fungal disease affecting Norway spruce in southern Finland. In approximately 90 % of cases the causal agent is Heterobasidion parviporum. Root and butt rot infections have not been reported in Finnish peatlands. However, the increase in logging operations in peatlands means there is a risk that the fungus will eventually spread to these areas. The aim of this study was to find out the impact of growing site on the resistance of Norway spruce to Heterobasidion parviporum infections. This was investigated by artificially inoculating H. parviporum to spruce trees in pristine mire, drained peatland and mineral soil and comparing the defence reactions. Additionally, the effect of genotype on resistance was studied by comparing the responses of spruce clones representing different geographic origins. The roots and stems of the trees to be sampled were wounded and inoculated with wood dowels pre-colonised by H. parviporum hyphae. The resulting necrosis around the point of inoculation was observed. It was presumed that increased length of necrosis indicates high susceptibility of the tree to the disease. The relationship between growth rate and host resistance was also studied. The results indicated that growing site does not have a statistically significant effect on host resistance. The average length of necrosis around the point of inoculation was 35 mm in pristine mire, 37 mm in drained peatland and 40 mm in mineral soil. It was observed that growth rate does not affect resistance, but that the genotype of the tree does have an effect. The most resistant spruce clone was the one with Russian origin. The results suggest that the spruce stands in peatlands are not more resistant to root and butt rot infections than those in mineral soil. These findings should be taken into consideration when logging peatland forests.

Time scales for transitions between free-energy minima of a dense hard-sphere system

Time scales associated with activated transitions between glassy metastable states of a free-energy functional appropriate for a dense hard-sphere system are calculated by using a new Monte Carlo method for the local density variables. In particular, we calculate the time the system, initially placed in a shallow glassy minimum of the free-energy, spends in the neighborhood of this minimum before making a transition to the basin of attraction of another free-energy minimum. This time scale is found to increase as the average density is increased. We find a crossover density near which this time scale increases very sharply and becomes longer than the longest times accessible in our simulation. This time scale does not show any evidence of increasing with sample size

Multiple scales without center manifold reductions for delay differential equations near Hopf bifurcations

We study small perturbations of three linear Delay Differential Equations (DDEs) close to Hopf bifurcation points. In analytical treatments of such equations, many authors recommend a center manifold reduction as a first step. We demonstrate that the method of multiple scales, on simply discarding the infinitely many exponentially decaying components of the complementary solutions obtained at each stage of the approximation, can bypass the explicit center manifold calculation. Analytical approximations obtained for the DDEs studied closely match numerical solutions.

Role of length scales on microwave thawing dynamics in 2D cylinders

Microwave (MW) thawing of 2D frozen cylinders exposed to uniform plane waves from one face, is modeled using the effective heat capacity formulation with the MW power obtained from the electric field equations. Computations are illustrated for tylose (23% methyl cellulose gel) which melts over a range of temperatures giving rise to a mushy zone. Within the mushy region the dielectric properties are functions of the liquid volume fraction. The resulting coupled, time dependent non-linear equations are solved using the Galerkin finite element method with a fixed mesh. Our method efficiently captures the multiple connected thawed domains that arise due to the penetration of MWs in the sample. For a cylinder of diameter D, the two length scales that control the thawing dynamics are D/D-p and D/lambda(m), where D-p and lambda(m) are the penetration depth and wavelength of radiation in the sample respectively. For D/D-p, D/lambda(m) much less than 1 power absorption is uniform and thawing occurs almost simultaneously across the sample (Regime I). For D/D-p much greater than 1 thawing is seen to occur from the incident face, since the power decays exponentially into the sample (Regime III). At intermediate values, 0.2 < D/D-p, D/lambda(m) < 2.0 (Regime II) thawing occurs from the unexposed face at smaller diameters, from both faces at intermediate diameters and from the exposed and central regions at larger diameters. Average power absorption during thawing indicates a monotonic rise in Regime I and a monotonic decrease in Regime III. Local maxima in the average power observed for samples in Regime II are due to internal resonances within the sample. Thawing time increases monotonically with sample diameter and temperature gradients in the sample generally increase from Regime I to Regime III. (C) 2002 Elsevier Science Ltd. All rights reserved.

Studies on the effects of test gas on the flow field around large angle blunt cone flying at hypersonic Mach number

The effect of the test gas on the flow field around a 120degrees apex angle blunt cone has been investigated in a shock tunnel at a nominal Mach number of 5.75. The shock standoff distance around the blunt cone was measured by an electrical discharge technique using both carbon dioxide and air as test gases. The forebody laminar convective heat transfer to the blunt cone was measured with platinum thin-film sensors in both air and carbon dioxide environments. An increase of 10 to 15% in the measured heat transfer values was observed with carbon dioxide as the test gas in comparison to air. The measured thickness of the shock layer along the stagnation streamline was 3.57 +/- 0.17 mm in air and 3.29 +/- 0.26 mm in carbon dioxide. The computed thickness of the shock layer for air and carbon dioxide were 3.98 mm and 3.02 mm, respectively. The observed increase in the measured heat transfer rates in carbon dioxide compared to air was due to the higher density ratio across the bow shock wave and the reduced shock layer thickness.

Electronic structure of ${\rm Ca}_{1-x}{\rm Sr}_x{\rm VO}_3$: A tale of two energy scales

We investigate the electronic structure of Ca1-xSrxVO3 using photoemission spectroscopy. Core level spectra establish an electronic phase separation at the surface, leading to a distinctly different surface electronic structure compared to the bulk. Analysis of the photoemission spectra of this system allowed us to separate the surface and bulk contributions. These results help us to understand properties related to two vastly differing energy scales, namely the low-energy scale of thermal excitations ( $\sim\!k_{\rm B}T$) and the high-energy scale related to Coulomb and other electronic interactions.

The destabilization of human GCAP1 by a proline to leucine mutation might cause cone-rod dystrophy

Guanylate cyclase activating protein-1 (GCAP1) is required for activation of retinal guanylate cyclase-1 (RetGC1), which is essential for recovery of photoreceptor cells to the dark state. In this paper, experimentally derived observations are reported that help in explaining why a proline→leucine mutation at position 50 of human GCAP1 results in cone–rod dystrophy in a family carrying this mutation. The primary amino acid sequence of wild-type GCAP1 was mutated using site-directed mutagenesis to give a leucine at position 50. In addition, serine replaced a glutamic acid residue at position 6 to promote N‐terminal myristoylation, yielding the construct GCAP1 E6S/P50L. The enzyme was over-expressed in Escherichia coli cells, isolated and purified before being used in assays with RetGC1, characterized by circular dichroism (CD) spectroscopy, and investigated for protease resistance and thermal stability. Assays of cyclic guanosine monophosphate (cGMP) synthesis from guanosine triphosphate by RetGC1 in the presence of E6S/P50L showed that E6S/P50L could activate RetGC1 and displayed similar calcium sensitivity to wild-type GCAP1. In addition, E6S/P50L and wild-type GCAP1 possess similar CD spectra. However, there was a marked increase in the susceptibility to protease degradation and also a reduction in the thermal stability of E6S/P50L as observed by both the cGMP assay and CD spectroscopy. It is therefore suggested that although GCAP1 E6S/P50L has a similar activity and calcium dependency profile to the wild-type GCAP1, its lower stability could reduce its cellular concentration, which would in turn alter [Ca2+] and result in death of cells.

Unsteady mixed convection flow from a rotating vertical cone with a magnetic field

An analysis is developed to study the unsteady mixed convection flow over a vertical cone rotating in an ambient fluid with a time-dependent angular velocity in the presence of a magnetic field. The coupled nonlinear partial differential equations governing the flow have been solved numerically using an implicit finite-difference scheme. The local skin friction coefficients in the tangential and azimuthal directions and the local Nusselt number increase with the time when the angular velocity of the-cone increases, but the reverse trend is observed for decreasing angular velocity. However, these are not mirror reflection of each other. The magnetic field reduces the skin friction coefficient in the tangential direction and also the Nusselt number, but it increases the skin friction coefficient in the azimuthal direction. The skin friction coefficients and the Nusselt number increase with the buoyancy force.

Estimation of missing data using windowed linear prediction in laterally truncated projection & in cone beam CT

In this paper, we address the reconstruction problem from laterally truncated helical cone-beam projections. The reconstruction problem from lateral truncation, though similar to that of interior radon problem, is slightly different from it as well as the local (lambda) tomography and pseudo-local tomography in the sense that we aim to reconstruct the entire object being scanned from a region-of-interest (ROI) scan data. The method proposed in this paper is a projection data completion approach followed by the use of any standard accurate FBP type reconstruction algorithm. In particular, we explore a windowed linear prediction (WLP) approach for data completion and compare the quality of reconstruction with the linear prediction (LP) technique proposed earlier.