Brain-like large scale cognitive networks and dynamics

A new approach to the study of the brain and its functions known as Human Connectomics has been recently established. Starting from magnetic resonance images (MRI) of brain scans, it is possible to identify the fibers that link brain areas and to build an adjacency matrix that connects these areas, thus creating the brain connectome. The topology of these networks provides a lot of information about the organizational structure of the brain (both structural and functional). Nevertheless this knowledge is rarely used to investigate the possible emerging brain dynamics linked to cognitive functions. In this work, we implement finite state models on neural networks to display the outcoming brain dynamics, using different types of networks, which correspond to diverse segmentation methods and brain atlases. From the simulations, we observe that the behavior of these systems is completely different from random and/or artificially generated networks. The emergence of stable structures, which might correspond to brain cognitive circuits, has also been detected.     

Influences of subgrid scale dynamics on resolvable scale statistics in large-eddy simulations

Recently, the -expansion and recursive renormalization group (RNG) theories as well as approximate inertial manifolds (AIM) have been exploited as means of systematically modeling subgrid scales in large-eddy simulations (LES). Although these theoretical approaches are rather complicated mathematically, their key approximations can be investigated using direct numerical simulations (DNS). In fact, the differences among these theories can be traced to whether they retain or neglect interactions between the subgrid-subgrid and subgrid-resolvable scales. In this paper, we focus on the influence of these two interactions on the evolution of the resolvable scales in LES: the effect^A which keeps only the interactions between the small and large scales; and, the effect^B which, on the other hand, keeps only the interactions among the subgrid-subgrid scales. The performance of these models is analyzed using the velocity fields of the direct numerical simulations. Specifically, our comparison is based on the analysis of the energy and enstrophy spectra, as well as higher-order statistics of the velocity and velocity derivatives. We found that the energy spectrum and higher-order statistics for the simulations with the effect^A (referred to, hereafter, as model^A) are in very good agreement with the filtered DNS. The comparison between the computations with effect^B (referred to, hereafter, as model^B) and the filtered DNS, however, is not satisfactory. Moreover, the decorrelation between the filtered DNS and model^A is much slower than that of the filtered DNS and model^B. Therefore, we conclude that the model^A, taking into acciunt the interactions between the subgrid and resolvable scales, is a faithful subgrid model for LES for the range of Reynolds numbers considered.     

Atomic force microscopy on chromosomes, chromatin and DNA: A review

The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA.     

Interorganellar DNA transfer in wheat: dynamics and phylogenetic origin

A homology search of wheat chloroplast (ct) and mitochondrial (mt) genomes identified 54 ctDNA segments that have homology with 66 mtDNA segments. The mtDNA segments were classified according to their origin: orthologs (prokaryotic origin), xenologs (interorganellar DNA transfer origin) and paralogs (intraorganellar DNA amplification origin). The 66 mtDNA sequences with homology to ctDNA segments included 14 paralogs, 18 orthologs and 34 xenologs. Analysis of the xenologs indicated that the DNA transfer occurred unidirectionally from the ct genome to the mt genome. The evolutionary timing of each interorganellar DNA transfer that generated a xenolog was estimated. This analysis showed that 2 xenologs originated early in green plant evolution, 4 in angiosperm evolution, 3 in monocotyledon evolution, 9 during cereal diversification and 8 in the evolution of wheat. Six other xenologs showed recurrent transfer from the ct to mt genomes in more than one taxon. The two remaining xenologs were uninformative on the evolutionary timing of their transfer. The wheat mt nad9 gene was found to be chimeric, consisting of the cereal nad9 gene and its 291 bp 5'-flanking region that included a 58 bp xenolog of the ct-ndhC origin.     

Loop dynamics in DNA denaturation

The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The long-time decay of the autocorrelation function is expressed in terms of the loop exponent c both for homopolymers and heteropolymers. This suggests an experimental method for measuring the exponent c using florescence correlation spectroscopy.     

Multiple-time scale accelerated molecular dynamics: addressing the small-barrier problem

We present a method for accelerated molecular-dynamics simulation in systems with rare-event dynamics that span a wide range of time scales. Using a variant of hyperdynamics, we detect, on the fly, groups of recurrent states connected by small energy barriers and we modify the potential-energy surface locally to consolidate them into large, coarse states. In this way, fast motion between recurrent states is treated within an equilibrium formalism and dynamics can be simulated over the longer time scale of the slow events. We apply the method to simulate cluster diffusion and the initial growth of Co on Cu(001),where time scales spanning more than 6 orders of magnitude are present, and show that the method correctly follows the slow events, so that much larger times can be simulated than with accelerated molecular dynamics alone.     

Bubble dynamics in double-stranded DNA

We report the first measurement of the dynamics of bubble formation in double-stranded DNA. Fluctuations of fluorescence of a synthetic DNA construct, internally tagged with a fluorophore and a quencher, are monitored by fluorescence correlation spectroscopy. The relaxation dynamics follow a multistate relaxation kinetics, with a characteristic time scale of 50 microseconds. A simple model of bubble dynamics based on constant zipping-unzipping rates is proposed to account for our experimental data. The role of different secondary structures stabilizing the open bubble is tested.     

DNA dynamics in a microchannel

An extended Brownian dynamics simulation method is used to characterize the dynamics of long DNA molecules flowing in microchannels. The relaxation time increases due to confinement in agreement with scaling predictions. During flow the molecules migrate toward the channel center line, and thereby segregate according to molecular weight. Capturing these effects requires the detailed incorporation of solvent flow in the simulation method, demonstrating the importance of hydrodynamic effects in the dynamics of confined macromolecules.     

Dye-sensitized solar cells: Atomic scale investigation of interface structure and dynamics

Recent progress in dye-sensitized solar cells(DSC) research is reviewed, focusing on atomic-scale investigations of the interface electronic structures and dynamical processes, including the structure of dye adsorption onto TiO2, ultrafast electron injection, hot-electron injection, multiple-exciton generation, and electron–hole recombination. Advanced experimental techniques and theoretical approaches are briefly summarized, and then progressive achievements in photovoltaic device optimization based on insights from atomic scale investigations are introduced. Finally, some challenges and opportunities for further improvement of dye solar cells are presented.     

Global organization of dynamics in oscillatory heterogeneous excitable media

An oscillatory heterogeneous excitable medium undergoes a transition from periodic target patterns to a bursting rhythm driven by the spontaneous initiation and termination of spiral waves as coupling or density is reduced. We illustrate these phenomena in monolayers of chick embryonic heart cells using calcium-sensitive fluorescent dyes. These results are modeled in a heterogeneous cellular automaton in which the neighborhood of interaction and cell density is modified. Parameters that give rise to bursting rhythms are organized in distinct zones in parameter space, leading to a global organization that should be applicable to the dynamics in a large class of excitable media.     

Image features in medical vibro-acoustography: in vitro and in vivo results

Vibro-acoustography is an imaging method based on audio-frequency harmonic vibrations induced in the object by the radiation force of focused ultrasound. The purpose of this study is to investigate features of vibro-acoustography images and manifestation of various tissue structures and calcifications in such images. Our motivation for this study is to pave the way for further in vitro and in vivo applications of vibro-acoustography. Here, vibro-acoustography images of excised prostate and in vivo breast are presented and compared with images obtained with other modalities. Resulting vibro-acoustography images obtained with a 3 MHz ultrasound transducer and at a vibration frequency of 50-60 kHz show soft tissue structures, tissue borders, and microcalcifications with high contrast, high resolution, and no speckle. It is concluded that vibro-acoustography offers features that may be valuable for diagnostic purposes.     

Toxicity of citrate-capped AuNPs: an in vitro and in vivo assessment

In this study, we show that 15 nm citrate-capped AuNPs exert a remarkable toxicity in living systems. The assessment was performed by using well-characterized AuNPs, the combination of in vitro and in vivo models (namely two different cell lines and Drosophila melanogaster), exposure to low dosages of nanoparticles (in the sub-nanomolar concentration range), along with the application of several biological assays to monitor different aspects of the toxic effects, such as viability, genotoxicity, and molecular biomarkers.     

Time scale bridging in atomistic simulation of slow dynamics: viscous relaxation and defect activation

Atomistic simulation methods are known for timescale limitations in resolving slow dynamical processes. Two well-known scenarios of slow dynamics are viscous relaxation in supercooled liquids and creep deformation in stressed solids. In both phenomena the challenge to theory and simulation is to sample the transition state pathways efficiently and follow the dynamical processes on long timescales. We present a perspective based on the biased molecular simulation methods such as metadynamics, autonomous basin climbing (ABC), strain-boost and adaptive boost simulations. Such algorithms can enable an atomic-level explanation of the temperature variation of the shear viscosity of glassy liquids, and the relaxation behavior in solids undergoing creep deformation. By discussing the dynamics of slow relaxation in two quite different areas of condensed matter science, we hope to draw attention to other complex problems where anthropological or geological-scale time behavior can be simulated at atomic resolution and understood in terms of micro-scale processes of molecular rearrangements and collective interactions. As examples of a class of phenomena that can be broadly classified as materials ageing, we point to stress corrosion cracking and cement setting as opportunities for atomistic modeling and simulations.     

Monomer dynamics in double- and single-stranded DNA polymers

We present the first measurements of the kinetics of random motion of individual monomers within large polymer coils. We use double- and single-stranded DNA (dsDNA and ssDNA) as models of semiflexible and flexible polymers, respectively. Fluorescence fluctuations of DNA fragments labeled specifically at a single position reveal the time dependence of the DNA monomer's mean-square displacement . The monomer motions within dsDNA and ssDNA coils are characterized by two qualitatively different kinetic regimes: close to proportional to t(2/3) for ssDNA and proportional to sqrt[t] for dsDNA. While the kinetic behavior of ssDNA is consistent with the generally accepted Zimm theory of polymer dynamics, the kinetic behavior of dsDNA monomers is in good agreement with the Rouse model.     

Stretching and relaxation dynamics in double stranded DNA

We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special attention to the opening–closing dynamics of double-stranded DNA molecules which are forced into non-equilibrium conformations. Mechanical stress imposed at one terminal end of the DNA molecule brings it into a partially opened configuration. We examine the subsequent relaxation dynamics connected with energy exchange processes between the various degrees of freedom and structural rearrangements leading to complete recombination to the double-stranded conformation. The similarities and differences between the relaxation dynamics for a planar ladder-like DNA molecule and a twisted one are discussed in detail. In this way we show that the attainment of a quasi-equilibrium regime proceeds faster in the case of the twisted DNA form than for its thus less flexible ladder counterpart. Furthermore we find that the velocity of the complete recombination of the DNA molecule is lower than the velocity imposed by the forcing unit which is in compliance with the experimental observations for the opening–closing cycle of DNA molecules.