Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution

Several time dependent fluorescence Stokes shift (TDFSS) experiments have reported a slow power law decay in the hydration dynamics of a DNA molecule. Such a power law has neither been observed in computer simulations nor in some other TDFSS experiments. Here we observe that a slow decay may originate from collective ion contribution because in experiments DNA is immersed in a buffer solution, and also from groove bound water and lastly from DNA dynamics itself. In this work we first express the solvation time correlation function in terms of dynamic structure factors of the solution. We use mode coupling theory to calculate analytically the time dependence of collective ionic contribution. A power law decay in seen to originate from an interplay between long-range probe-ion direct correlation function and ion-ion dynamic structure factor. Although the power law decay is reminiscent of Debye-Falkenhagen effect, yet solvation dynamics is dominated by ion atmosphere relaxation times at longer length scales (small wave number) than in electrolyte friction. We further discuss why this power law may not originate from water motions which have been computed by molecular dynamics simulations. Finally, we propose several experiments to check the prediction of the present theoretical work.

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.

Unusual Fragility and Cooperativity in Glass-Forming and Crystalline PVDF/PMMA Blends in the Presence of Multiwall Carbon Nanotubes

Poly(vinylidene fluoride) (PVDF) and poly(methyl methacrylate) (PMMA) are completely miscible below 50 wt % PVDF in the blends. In this work, an attempt was made to understand the fragility/cooperativity relation in glass-forming and crystalline blends of PVDF/PMMA and in the presence of a heteronucleating agent, multiwall carbon nanotubes (CNTs). Hence, three representative blends were chosen: a completely amorphous (10/90 by wt, PVDF/PMMA), on the verge of amorphous miscibility (50/50 by wt, PVDF/PMMA), and crystalline (60/40 by wt, PVDF/PMMA) blends. The intermolecular cooperativity/coupling, fragility, and configurational entropy near the glass transition temperature (T-g) were studied using differential scanning calorimetry (DSC) and broadband dielectric relaxation spectroscopy (DRS). It was observed that the blends with higher concentration of PMMA were more fragile (fragility index m = 141) and those with higher concentration of PVDF were more strong (m = 78). Interestingly, the coupling was less in the glass-forming blends (10/90 by wt, PVDF/PMMA) than the crystalline blends as manifested from DRS. This observation was also supported by DSC measurements which reflected that the cooperative rearranging region (CRR) existed over a smaller length scales in fragile blends as compared to strong blends, possibly due to restricted amorphous mobility. This effect was more prominent in the presence of CNTs, in particular for 50/50 (by wt) and 60/40 (by wt) PVDF/PMMA blends. Further, the configurational entropy, as manifested from DRS, decreased significantly in the strong blends in striking contrast to the fragile blends, supported by DSC, which manifested in an increase in the volume of cooperativity in the strong blends. The higher coupling in the crystalline blends can be attributed to good packing of the amorphous regions. While this is understood for crystalline blends (60/40 by wt, PVDF/PMMA), it is envisaged that enhanced dynamic heterogeneity is accountable for increased coupling in the case of blends which are on the verge of amorphous miscibility (50/50 by wt, PVDF/PMMA). The latter is also supported by broad relaxations near the T-g in DRS. Interestingly, the intermolecular coupling in the blends in the presence of CNTs has reduced, though the potential energy barrier hindering the rearrangement of CRR is lower than the blends without CNTs. In addition, the amorphous packing is not as effective as the blends without CNTs. This is manifested from reduced volume of cooperativity in particular, for 50/50 (by wt) and 60/40 (by wt) blends.

A method for coupling the phase-field model based on a grand-potential formalism to thermodynamic databases

In this paper we derive an approach for the effective utilization of thermodynamic data in phase-field simulations. While the most widely used methodology for multi-component alloys is following the work by Eiken et al. (2006), wherein, an extrapolative scheme is utilized in conjunction with the TQ interface for deriving the driving force for phase transformation, a corresponding simplistic method based on the formulation of a parabolic free-energy model incorporating all the thermodynamics has been laid out for binary alloys in the work by Folch and Plapp (2005). In the following, we extend this latter approach for multi-component alloys in the framework of the grand-potential formalism. The coupling is applied for the case of the binary eutectic solidification in the Cr-Ni alloy and two-phase solidification in the ternary eutectic alloy (Al-Cr-Ni). A thermodynamic justification entails the basis of the formulation and places it in context of the bigger picture of Integrated Computational Materials Engineering. (C) 2015 Elsevier Ltd. All rights reserved.

Synthesis of Novel Benzofuran-Gathered C-2,4,6-substituted Pyrimidine Derivatives Conjugated by Sulfonyl Chlorides: Orally Bioavailable, Selective, Effective Antioxidants and Antimicrobials Drug Candidates

In the present study, we have made an effort to develop the novel synthetic antioxidants and antimicrobials with improved potency. The novel benzofuran-gathered C-2,4,6-substituted pyrimidine derivatives 5a, 5b, 5c, 5d, 5e, 5f, 6a, 6b, 6c, 6d, 6e, 6f, 7a, 7b, 7c, 7d, 7e, 7f, 8a, 8b, 8c, 8d, 8e, 8f, 9a, 9b, 9c, 9d, 9e, 9f were synthesized by simple and efficient four-step reaction pathway. Initially, o-alkyl derivative of salicylaldehyde readily furnish corresponding 2-acetyl benzofuran 2 in good yield, upon the treatment with potassium tertiary butoxide in the presence of molecular sieves. Further, Claisen-Schmidt condensation with aromatic aldehydes via treatment with thiourea followed by coupling reaction with different sulfonyl chlorides afforded target compounds. The structures of newly synthesized compounds were confirmed by IR, H-1 NMR, C-13 NMR, mass, and elemental analysis and further screened for their antioxidant and antimicrobial activities. The results showed that the synthesized compounds 8b, 8e, 9b, and 9e produced significant antioxidant activity with 50% inhibitory concentration higher than that of reference, whereas compounds 7d and 7c produced dominant antimicrobial activity at concentrations 1.0 and 0.5mg/mL compared with standard Gentamicin and Nystatin, respectively.

Baryon squishing in synthetic dimensions by effective SU(M) gauge fields

The ``synthetic dimension'' proposal A. Celi et al., Phys. Rev. Lett. 112, 043001 (2014)] uses atoms with M internal states (''flavors'') in a one-dimensional (1D) optical lattice, to realize a hopping Hamiltonian equivalent to the Hofstadter model (tight-binding model with a given magnetic flux per plaquette) on an M-sites-wide square lattice strip. We investigate the physics of SU(M) symmetric interactions in the synthetic dimension system. We show that this system is equivalent to particles with SU(M) symmetric interactions] experiencing an SU(M) Zeeman field at each lattice site and a non-Abelian SU(M) gauge potential that affects their hopping. This equivalence brings out the possibility of generating nonlocal interactions between particles at different sites of the optical lattice. In addition, the gauge field induces a flavor-orbital coupling, which mitigates the ``baryon breaking'' effect of the Zeeman field. For M particles, concomitantly, the SU(M) singlet baryon which is site localized in the usual 1D optical lattice, is deformed to a nonlocal object (''squished baryon''). We conclusively demonstrate this effect by analytical arguments and exact (numerical) diagonalization studies. Our study promises a rich many-body phase diagram for this system. It also uncovers the possibility of using the synthetic dimension system to laboratory realize condensed-matter models such as the SU(M) random flux model, inconceivable in conventional experimental systems.

Length scales in glass-forming liquids and related systems: a review

The central problem in the study of glass-forming liquids and other glassy systems is the understanding of the complex structural relaxation and rapid growth of relaxation times seen on approaching the glass transition. A central conceptual question is whether one can identify one or more growing length scale(s) associated with this behavior. Given the diversity of molecular glass-formers and a vast body of experimental, computational and theoretical work addressing glassy behavior, a number of ideas and observations pertaining to growing length scales have been presented over the past few decades, but there is as yet no consensus view on this question. In this review, we will summarize the salient results and the state of our understanding of length scales associated with dynamical slow down. After a review of slow dynamics and the glass transition, pertinent theories of the glass transition will be summarized and a survey of ideas relating to length scales in glassy systems will be presented. A number of studies have focused on the emergence of preferred packing arrangements and discussed their role in glassy dynamics. More recently, a central object of attention has been the study of spatially correlated, heterogeneous dynamics and the associated length scale, studied in computer simulations and theoretical analysis such as inhomogeneous mode coupling theory. A number of static length scales have been proposed and studied recently, such as the mosaic length scale discussed in the random first-order transition theory and the related point-to-set correlation length. We will discuss these, elaborating on key results, along with a critical appraisal of the state of the art. Finally we will discuss length scales in driven soft matter, granular fluids and amorphous solids, and give a brief description of length scales in aging systems. Possible relations of these length scales with those in glass-forming liquids will be discussed.

Multiscale Coupling in Complex Mechanical Systems

Multiscale coupling attracts broad interests from mechanics, physics and chemistry to biology. The diversity and coupling of physics at different scales are two essential features of multiscale problems in far-from-equilibrium systems. The two features present fundamental difficulties and are great challenges to multiscale modeling and simulation. The theory of dynamical system and statistical mechanics provide fundamental tools for the multiscale coupling problems. The paper presents some closed multiscale formulations, e.g., the mapping closure approximation, multiscale large-eddy simulation and statistical mesoscopic damage mechanics, for two typical multiscale coupling problems in mechanics, that is, turbulence in fluids and failure in solids. It is pointed that developing a tractable, closed nonequilibrium statistical theory may be an effective approach to deal with the multiscale coupling problems. Some common characteristics of the statistical theory are discussed.

A generalized model for the effective thermal conductivity of porous media based on self-similarity

A generalized model for the effective thermal conductivity of porous media is derived based on the fact that statistical self-similarity exists in porous media. The proposed model assumes that porous media consist of two portions: randomly distributed non-touching particles and self-similarly distributed particles contacting each other with resistance. The latter are simulated by Sierpinski carpets with side length L = 13 and cutout size C = 3, 5, 7 and 9, respectively, depending upon the porosity concerned. Recursive formulae are presented and expressed as a function of porosity, ratio of areas, ratio of component thermal conductivities and contact resistance, and there is no empirical constant and every parameter has a clear physical meaning. The model predictions are compared with the existing experimental data, and good agreement is found in a wide range of porosity of 0.14-0.80, and this verifies the validity of the proposed model.

“Deborah Numbers”, Coupling Multiple Space and Time Scales and Governing Damage Evolution to Failure

Two different spatial levels are involved concerning damage accumulation to eventual failure. nucleation and growth rates of microdamage nN* and V*. It is found that the trans-scale length ratio c*/L does not directly affect the process. Instead, two independent dimensionless numbers: the trans-scale one * * ( V*)including the * **5 * N c V including mesoscopic parameters only, play the key role in the process of damage accumulation to failure. The above implies that there are three time scales involved in the process: the macroscopic imposed time scale tim = /a and two meso-scopic time scales, nucleation and growth of damage, (* *4) N N t =1 n c and tV=c*/V*. Clearly, the dimensionless number De*=tV/tim refers to the ratio of microdamage growth time scale over the macroscopically imposed time scale. So, analogous to the definition of Deborah number as the ratio of relaxation time over external one in rheology. Let De be the imposed Deborah number while De represents the competition and coupling between the microdamage growth and the macroscopically imposed wave loading. In stress-wave induced tensile failure (spallation) De* < 1, this means that microdamage has enough time to grow during the macroscopic wave loading. Thus, the microdamage growth appears to be the predominate mechanism governing the failure. Moreover, the dimensionless number D* = tV/tN characterizes the ratio of two intrinsic mesoscopic time scales: growth over nucleation. Similarly let D be the “intrinsic Deborah number”. Both time scales are relevant to intrinsic relaxation rather than imposed one. Furthermore, the intrinsic Deborah number D* implies a certain characteristic damage. In particular, it is derived that D* is a proper indicator of macroscopic critical damage to damage localization, like D* ∼ (10–3~10–2) in spallation. More importantly, we found that this small intrinsic Deborah number D* indicates the energy partition of microdamage dissipation over bulk plastic work. This explains why spallation can not be formulated by macroscopic energy criterion and must be treated by multi-scale analysis.

An evaluation of length-frequency sampling procedures and subsequent data analysis for purse seine-caught yellowfin tuna in the Eastern Pacific Ocean

ENGLISH: A two-stage sampling design is used to estimate the variances of the numbers of yellowfin in different age groups caught in the eastern Pacific Ocean. For purse seiners, the primary sampling unit (n) is a brine well containing fish from a month-area stratum; the number of fish lengths (m) measured from each well are the secondary units. The fish cannot be selected at random from the wells because of practical limitations. The effects of different sampling methods and other factors on the reliability and precision of statistics derived from the length-frequency data were therefore examined. Modifications are recommended where necessary. Lengths of fish measured during the unloading of six test wells revealed two forms of inherent size stratification: 1) short-term disruptions of existing pattern of sizes, and 2) transition zones between long-term trends in sizes. To some degree, all wells exhibited cyclic changes in mean size and variance during unloading. In half of the wells, it was observed that size selection by the unloaders induced a change in mean size. As a result of stratification, the sequence of sizes removed from all wells was non-random, regardless of whether a well contained fish from a single set or from more than one set. The number of modal sizes in a well was not related to the number of sets. In an additional well composed of fish from several sets, an experiment on vertical mixing indicated that a representative sample of the contents may be restricted to the bottom half of the well. The contents of the test wells were used to generate 25 simulated wells and to compare the results of three sampling methods applied to them. The methods were: (1) random sampling (also used as a standard), (2) protracted sampling, in which the selection process was extended over a large portion of a well, and (3) measuring fish consecutively during removal from the well. Repeated sampling by each method and different combinations indicated that, because the principal source of size variation occurred among primary units, increasing n was the most effective way to reduce the variance estimates of both the age-group sizes and the total number of fish in the landings. Protracted sampling largely circumvented the effects of size stratification, and its performance was essentially comparable to that of random sampling. Sampling by this method is recommended. Consecutive-fish sampling produced more biased estimates with greater variances. Analysis of the 1988 length-frequency samples indicated that, for age groups that appear most frequently in the catch, a minimum sampling frequency of one primary unit in six for each month-area stratum would reduce the coefficients of variation (CV) of their size estimates to approximately 10 percent or less. Additional stratification of samples by set type, rather than month-area alone, further reduced the CV's of scarce age groups, such as the recruits, and potentially improved their accuracy. The CV's of recruitment estimates for completely-fished cohorts during the 198184 period were in the vicinity of 3 to 8 percent. Recruitment estimates and their variances were also relatively insensitive to changes in the individual quarterly catches and variances, respectively, of which they were composed. SPANISH: Se usa un diseño de muestreo de dos etapas para estimar las varianzas de los números de aletas amari11as en distintos grupos de edad capturados en el Océano Pacifico oriental. Para barcos cerqueros, la unidad primaria de muestreo (n) es una bodega de salmuera que contenía peces de un estrato de mes-área; el numero de ta11as de peces (m) medidas de cada bodega es la unidad secundaria. Limitaciones de carácter practico impiden la selección aleatoria de peces de las bodegas. Por 10 tanto, fueron examinados los efectos de distintos métodos de muestreo y otros factores sobre la confiabilidad y precisión de las estadísticas derivadas de los datos de frecuencia de ta11a. Se recomiendan modificaciones donde sean necesarias. Las ta11as de peces medidas durante la descarga de seis bodegas de prueba revelaron dos formas de estratificación inherente por ta11a: 1) perturbaciones a corto plazo en la pauta de ta11as existente, y 2) zonas de transición entre las tendencias a largo plazo en las ta11as. En cierto grado, todas las bodegas mostraron cambios cíclicos en ta11a media y varianza durante la descarga. En la mitad de las bodegas, se observo que selección por ta11a por los descargadores indujo un cambio en la ta11a media. Como resultado de la estratificación, la secuencia de ta11as sacadas de todas las bodegas no fue aleatoria, sin considerar si una bodega contenía peces de un solo lance 0 de mas de uno. El numero de ta11as modales en una bodega no estaba relacionado al numero de lances. En una bodega adicional compuesta de peces de varios lances, un experimento de mezcla vertical indico que una muestra representativa del contenido podría estar limitada a la mitad inferior de la bodega. Se uso el contenido de las bodegas de prueba para generar 25 bodegas simuladas y comparar los resultados de tres métodos de muestreo aplicados a estas. Los métodos fueron: (1) muestreo aleatorio (usado también como norma), (2) muestreo extendido, en el cual el proceso de selección fue extendido sobre una porción grande de una bodega, y (3) medición consecutiva de peces durante la descarga de la bodega. EI muestreo repetido con cada método y distintas combinaciones de n y m indico que, puesto que la fuente principal de variación de ta11a ocurría entre las unidades primarias, aumentar n fue la manera mas eficaz de reducir las estimaciones de la varianza de las ta11as de los grupos de edad y el numero total de peces en los desembarcos. El muestreo extendido evito mayormente los efectos de la estratificación por ta11a, y su desempeño fue esencialmente comparable a aquel del muestreo aleatorio. Se recomienda muestrear con este método. El muestreo de peces consecutivos produjo estimaciones mas sesgadas con mayores varianzas. Un análisis de las muestras de frecuencia de ta11a de 1988 indico que, para los grupos de edad que aparecen con mayor frecuencia en la captura, una frecuencia de muestreo minima de una unidad primaria de cada seis para cada estrato de mes-área reduciría los coeficientes de variación (CV) de las estimaciones de ta11a correspondientes a aproximadamente 10% 0 menos. Una estratificación adicional de las muestras por tipo de lance, y no solamente mes-área, redujo aun mas los CV de los grupos de edad escasos, tales como los reclutas, y mejoró potencialmente su precisión. Los CV de las estimaciones del reclutamiento para las cohortes completamente pescadas durante 1981-1984 fueron alrededor de 3-8%. Las estimaciones del reclutamiento y sus varianzas fueron también relativamente insensibles a cambios en las capturas de trimestres individuales y las varianzas, respectivamente, de las cuales fueron derivadas. (PDF contains 70 pages)

Asymptotic scaling in the two-dimensional O(3) Nonlinear sigma model: a Monte Carlo study on parallel computers

We investigate the 2d O(3) model with the standard action by Monte Carlo simulation at couplings β up to 2.05. We measure the energy density, mass gap and susceptibility of the model, and gather high statistics on lattices of size L ≤ 1024 using the Floating Point Systems T-series vector hypercube and the Thinking Machines Corp.'s Connection Machine 2. Asymptotic scaling does not appear to set in for this action, even at β = 2.10, where the correlation length is 420. We observe a 20% difference between our estimate m/Λ^─_(Ms) = 3.52(6) at this β and the recent exact analytical result . We use the overrelaxation algorithm interleaved with Metropolis updates and show that decorrelation time scales with the correlation length and the number of overrelaxation steps per sweep. We determine its effective dynamical critical exponent to be z' = 1.079(10); thus critical slowing down is reduced significantly for this local algorithm that is vectorizable and parallelizable.

We also use the cluster Monte Carlo algorithms, which are non-local Monte Carlo update schemes which can greatly increase the efficiency of computer simulations of spin models. The major computational task in these algorithms is connected component labeling, to identify clusters of connected sites on a lattice. We have devised some new SIMD component labeling algorithms, and implemented them on the Connection Machine. We investigate their performance when applied to the cluster update of the two dimensional Ising spin model.

Finally we use a Monte Carlo Renormalization Group method to directly measure the couplings of block Hamiltonians at different blocking levels. For the usual averaging block transformation we confirm the renormalized trajectory (RT) observed by Okawa. For another improved probabilistic block transformation we find the RT, showing that it is much closer to the Standard Action. We then use this block transformation to obtain the discrete β-function of the model which we compare to the perturbative result. We do not see convergence, except when using a rescaled coupling β_E to effectively resum the series. For the latter case we see agreement for m/ Λ^─_(Ms) at , β = 2.14, 2.26, 2.38 and 2.50. To three loops m/Λ^─_(Ms) = 3.047(35) at β = 2.50, which is very close to the exact value m/ Λ^─_(Ms) = 2.943. Our last point at β = 2.62 disagrees with this estimate however.

Space-frequency coupling, conical waves, and small-scale filamentation in water

Numerical simulations of fs laser propagation in water have been made to explain the small-scale filaments in water we have observed by a nonlinear fluorescence technique. Some analytical descriptions combined with numerical simulations show that a space-frequency coupling mainly from the interplay among self-phase modulation, dispersion and phase mismatching will reshape the laser beam into a conical wave which plays a major role of energy redistribution and can prevent laser beam from self-guiding over a long distance. An effective group velocity dispersion is introduced to explain the pulse broadening and compression in the filamentation. (c) 2005 American Institute of Physics.

Parity-dependent State Engineering and Tomography in the ultrastrong coupling regime

Reaching the strong coupling regime of light-matter interaction has led to an impressive development in fundamental quantum physics and applications to quantum information processing. Latests advances in different quantum technologies, like superconducting circuits or semiconductor quantum wells, show that the ultrastrong coupling regime (USC) can also be achieved, where novel physical phenomena and potential computational benefits have been predicted. Nevertheless, the lack of effective decoupling mechanism in this regime has so far hindered control and measurement processes. Here, we propose a method based on parity symmetry conservation that allows for the generation and reconstruction of arbitrary states in the ultrastrong coupling regime of light-matter interactions. Our protocol requires minimal external resources by making use of the coupling between the USC system and an ancillary two-level quantum system.

Variation in trawl geometry due to unequal warp length

Survey standardization procedures can reduce the variability in trawl catch efficiency thus producing more precise estimates of biomass. One such procedure, towing with equal amounts of trawl warp on both sides of the net, was experimentally investigated for its importance in determining optimal trawl geometry and for evaluating the effectiveness of the recent National Oceanic and Atmospheric Administration (NOAA) national protocol on accurate measurement of trawl warps. This recent standard for measuring warp length requires that the difference between warp lengths can be no more than 4% of the distance between the otter doors measured along the bridles and footrope. Trawl performance data from repetitive towing with warp differentials of 0, 3, 5, 7, 9, 11, and 20 m were analyzed for their effect on three determinants of flatfish catch efficiency: footrope distance off-bottom, bridle length in contact with the bottom, and area swept by the net. Our results indicated that the distortion of the trawl caused by asymmetry in trawl warp length could have a negative inf luence on flatfish catch efficiency. At a difference of 7 m in warp length, the NOAA 4% threshold value for the 83112 Eastern survey trawl used in our study, we found no effect on the acous-tic-based measures of door spread, wing spread, and headrope height off-bottom. However, the sensitivity of the trawl to 7 m of warp offset could be seen as footrope distances off-bottom increased slightly (particularly in the center region of the net where flatfish escapement is highest), and as the width of the bridle path responsible for flatfish herding, together with the effective net width, was reduced. For this survey trawl, a NOAA threshold value of 4% should be considered a maximum. A more conservative value (less than 4%) would likely reduce potential bias in estimates of relative abundance caused by large differences in warp length approaching 7 m.