Criteria for minimal model of driven polymer translocation.

While the characteristics of the driven translocation for asymptotically long polymers are well understood, this is not the case for finite-sized polymers, which are relevant for real-world experiments and simulation studies. Most notably, the behavior of the exponent α, which describes the scaling of the translocation time with polymer length, when the driving force fp in the pore is changed, is under debate. By Langevin dynamics simulations of regular and modified translocation models using the freely jointed-chain polymer model we find that a previously reported incomplete model, where the trans side and fluctuations were excluded, gives rise to characteristics that are in stark contradiction with those of the complete model, for which α increases with fp. Our results suggest that contribution due to fluctuations is important. We construct a minimal model where dynamics is completely excluded to show that close alignment with a full translocation model can be achieved. Our findings set very stringent requirements for a minimal model that is supposed to describe the driven polymer translocation correctly.

Dynamics of polymer ejection from capsid.

Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the ejection times scale with polymer length, τ ∼ N(α). We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) ρ inside the capsid. For very low densities ρ ≤ 0.002 the polymer is only weakly confined by the capsid, and we measure α = 1.33, which is close to α=1.4 obtained for polymer translocation. At intermediate densities the scaling exponents α = 1.25 and 1.21 for ρ = 0.01 and 0.02, respectively. These scalings are in accord with a crude derivation for the lower limit α = 1.2. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, ρ ⪆ 0.25. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.

Sedimentation of knotted polymers.

We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number n(c) of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov et al. [J. Mol. Biol. 267, 299 (1997)]. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration R(g)(-1), more specifically with the inverse of the R(g) component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, R(g)(-1) remains to a good precision linearly dependent on n(c). Therefore, R(g)(-1) is a good measure of a knot's complexity.

Mild cognitive impairment associates with concurrent decreases in serum cholesterol and cholesterol-related lipoprotein subclasses.

BACKGROUND AND OBJECTIVE: Accumulating evidence suggests that serum lipids are associated with cognitive decline and dementias. However, majority of the existing information concerns only serum total cholesterol (TC) and data at the level of lipoprotein fractions and subclasses is limited. The aim of this study was to explore the levels and trends of main cholesterol and triglyceride measures and eight lipoprotein subclasses during normal aging and the development of mild cognitive impairment by following a group of elderly for six years. DESIGN: Longitudinal. SETTING: City of Kuopio, Finland. PARTICIPANTS: 45 elderly individuals of which 20 developed mild cognitive impairment (MCI) during the follow-up. MEASUREMENTS: On each visit participants underwent an extensive neuropsychological and clinical assessment. Lipoprotein levels were measured via 1H NMR from native serum samples. RESULTS: Serum cholesterol and many primarily cholesterol-associated lipoprotein measures clearly decreased in MCI while the trends were increasing for those elderly people who maintained normal cognition. CONCLUSION: These findings suggest that a decreasing trend in serum cholesterol measures in elderly individuals may suffice as an indication for more detailed inspection for potential signs of cognitive decline.

Event distributions of polymer translocation.

We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of the process. We extract at a high length scale resolution distributions of polymer segments that continuously traverse through a nanoscale pore. The obtained log-normal distributions together with the characteristics of polymer translocation suggest that it is describable as a multiplicative stochastic process. In spite of its clear out-of-equilibrium nature the forced translocation is surprisingly similar to the unforced case. We find forms for the distributions almost unaltered with a common cut-off length. We show that the individual short-segment and short-time movements inside the pore give the scaling relations τ∼Nα and τ∼f-ß for the polymer translocation.

Small but slow world: how network topology and burstiness slow down spreading.

While communication networks show the small-world property of short paths, the spreading dynamics in them turns out slow. Here, the time evolution of information propagation is followed through communication networks by using empirical data on contact sequences and the susceptible-infected model. Introducing null models where event sequences are appropriately shuffled, we are able to distinguish between the contributions of different impeding effects. The slowing down of spreading is found to be caused mainly by weight-topology correlations and the bursty activity patterns of individuals.

Unforced polymer translocation compared to the forced case.

We present results for unforced polymer translocation from simulations using Langevin dynamics in two dimensions (2D) to four dimensions and stochastic rotation dynamics supporting hydrodynamic modes in three dimensions (3D). We compare our results to forced translocation and a simplified model where the polymer escapes from an infinite pore. The simple model shows that the scaling behavior of unforced translocation is independent of the dimension of the side to which the polymer is translocating. We find that, unlike its forced counterpart, unforced translocation dynamics is insensitive to pore design. Hydrodynamics is seen to markedly speed up the unforced translocation process but not to affect the scaling relations. Average mean-squared displacement shows scaling with average transition time in unforced but not in forced translocation. The waiting-time distribution in unforced translocation follows closely Poissonian distribution. Our measured transfer probabilities align well with those obtained from an equilibrium theory in 3D, but somewhat worse in 2D, where a polymer's relaxation toward equilibrium with respect to its translocation time is slower. Consequently, in stark contrast to forced translocation, unforced translocation is seen to remain close to equilibrium and shows clear universality.

Pore-polymer interaction reveals nonuniversality in forced polymer translocation.

We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced translocation characteristics significantly in the biologically relevant range of the pore force, i.e., the driving force. Details of the model are shown to change even the obtained scaling relations, which is a strong indication of strongly out-of-equilibrium dynamics in the computational studies which have not yet succeeded in addressing the characteristics of the forced translocation for biopolymers at realistic length scale.

Broad lifetime distributions for ordering dynamics in complex networks.

We search for conditions under which a characteristic time scale for ordering dynamics toward either of two absorbing states in a finite complex network of interactions does not exist. With this aim, we study random networks and networks with mesoscale community structure built up from randomly connected cliques. We find that large heterogeneity at the mesoscale level of the network appears to be a sufficient mechanism for the absence of a characteristic time for the dynamics. Such heterogeneity results in dynamical metastable states that survive at any time scale.

Analysis of DNA elasticity.

With a model that incorporates hydrodynamics directly, we show that flow experiments can be used for detecting some characteristics of the DNA elasticity which manifest themselves clearly at large length scales but cannot be observed by mechanical forcing experiments even at very small length scales. By systematic analysis, the conclusiveness of different experimental methods is evaluated. For the wormlike chain, confirmed as the correct model for DNA, we find an underlying scaling relation between its extension and flow velocity of the form L(p) approximately v(0.155), which emphasizes the significance of hydrodynamics.

Critical evaluation of the computational methods used in the forced polymer translocation.

In forced polymer translocation, the average translocation time tau scales with respect to pore force f and polymer length N as tau approximately f;{-1}N;{beta} . We demonstrate that an artifact in the Metropolis Monte Carlo method resulting in breakage of the force scaling with large f may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent beta

Structure and tie strengths in mobile communication networks.

Electronic databases, from phone to e-mails logs, currently provide detailed records of human communication patterns, offering novel avenues to map and explore the structure of social and communication networks. Here we examine the communication patterns of millions of mobile phone users, allowing us to simultaneously study the local and the global structure of a society-wide communication network. We observe a coupling between interaction strengths and the network's local structure, with the counterintuitive consequence that social networks are robust to the removal of the strong ties but fall apart after a phase transition if the weak ties are removed. We show that this coupling significantly slows the diffusion process, resulting in dynamic trapping of information in communities and find that, when it comes to information diffusion, weak and strong ties are both simultaneously ineffective.

Are the structures of twist grain boundaries in silicon ordered at 0 K?

Contrary to previous simulation results on the existence of amorphous intergranular films at high-angle twist grain boundaries (GBs) in elemental solids such as silicon, recent experimental results imply structural order in some high-angle boundaries. With a novel protocol for simulating twist GBs, which allows the number of atoms at the boundary to vary, we have found new low-energy ordered structures. We give a detailed exposition of the results for the simplest boundary. The validity of our results is confirmed by first-principles calculations.

Hybrid Monte Carlo-molecular dynamics algorithm for the study of islands and step edges on semiconductor surfaces: application to Si/Si (001).

A classical, hybrid Monte Carlo-molecular dynamic (MC-MD) algorithm is introduced for the study of phenomena like two-dimensional (2D) island stability or step-edge evolution on semiconductor surfaces. This method presents the advantages of working off lattice and utilizing bulk-fitted potentials. It is based on the introduction of collective moves, such as dimer jumps, in the MC algorithm. MD-driven local relaxations are considered as trial moves for the MC. The algorithm is applied to the analysis of 2D Si islands on Si(001). Results on early stages of island formation, island stability versus temperature and system size, and step-edge evolution are presented. In all cases good qualitative agreement with experimental results is found.

Dynamics of market correlations: taxonomy and portfolio analysis.

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the "asset tree" has been studied in order to reflect the financial market taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer. During crashes, due to the strong global correlation in the market, the tree shrinks topologically, and this is shown by a low value of the mean occupation layer. The tree seems to have a scale-free structure where the scaling exponent of the degree distribution is different for "business as usual" and "crash" periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects such as the window size dependence of the investigated quantities are also discussed.

Time-dependent cross-correlations between different stock returns: a directed network of influence.

We study the time-dependent cross-correlations of stock returns, i.e., we measure the correlation as the function of the time shift between pairs of stock return time series using tick-by-tick data. We find a weak but significant effect showing that in many cases the maximum correlation appears at nonzero time shift, indicating directions of influence between the companies. Due to the weakness of this effect and the shortness of the characteristic time (of the order of a few minutes), our findings are compatible with market efficiency. The interaction of companies defines a directed network of influence.

Scaling of random spreading in small world networks.

In this study we have carried out computer simulations of random walks on Watts-Strogatz-type small world networks and measured the mean number of visited sites and the return probabilities. These quantities were found to obey scaling behavior with intuitively reasoned exponents as long as the probability p of having a long range bond was sufficiently low.

Effect of anisotropy on the instability of crack propagation

Dynamics of fracture is investigated in an anisotropic two-dimensional Born-Maxwell model by numerical simulations. From previous studies it is known that the isotropic model shows crack branching and velocity oscillations of the propagating main crack above a critical velocity, similarly with experimental findings in some brittle materials. Here we present studies in which anisotropy has been introduced to the model system. Anisotropy is found to have significant effects on crack propagation and on the pattern it forms. In the case of symmetric anisotropy (relative to the crack direction) we found changes in velocity oscillation and side branching properties. In the case of asymmetric anisotropy two kinds of periodicities occur and strong anisotropy causes different branch patterns to form at two sides of the main crack. In addition, the role of disorder through distributed spring constants has been studied for both types of anisotropy. Finally a simple exactly solvable model for investigating the initial stages of crack branching has been developed and analyzed.

[The role of chemotherapy in treatment of nephroblastoma in children. Report of the Polish Pediatric Group re. treatments of solid tumors]. / Udzial chemioterapii w leczeniu nerczaka zarodkowego u dzieci. Raport Zespolu Polskiej Grupy Pediatrycznej ds. Leczenia Guzów Litych.

Retrospective analysis of chemotherapy results of children with nephroblastoma was performed in 220 patients aged from 1 yr to 14 yrs of live in 12 centers. Stage I nephroblastoma was documented in 24.5% but stage II--in 55.3%. Histologically 74.6% cases were diagnosed as medium malignant and 12.7%--high malignant. Therapy results were similar to observed in other centers.