Polymer dynamics in time-dependent periodic potentials

Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations for computing the stationary state properties of molecules with internal structure in time-dependent periodic potentials on a lattice. As an example, we consider standard and modified Rubinstein-Duke polymers and calculate their mean drift and effective diffusion coefficient in the two-state non-symmetric flashing potential and symmetric traveling potential. Rich non-linear behavior of these observables is found. By varying the polymer length, we find current inversions caused by the rebound effect that is only present for molecules with internal structure. These results depend strongly on the polymer type. We also notice increased transport coherence for longer polymers.Comment: 22 pages, 7 figure

Optimizing methods for linking cinematic features to fMRI data

One of the challenges of naturalistic neurosciences using movie-viewing experiments is how to interpret observed brain activations in relation to the multiplicity of time-locked stimulus features. As previous studies have shown less inter-subject synchronization across viewers of random video footage than story-driven films, new methods need to be developed for analysis of less story-driven contents. To optimize the linkage between our fMRI data collected during viewing of a deliberately non-narrative silent film 'At Land' by Maya Deren (1944) and its annotated content, we combined the method of elastic-net regularization with the model-driven linear regression and the well-established data-driven independent component analysis (ICA) and inter-subject correlation (ISC) methods. In the linear regression analysis, both IC and region-of-interest (ROI) time-series were fitted with time-series of a total of 36 binary-valued and one real-valued tactile annotation of film features. The elastic-net regularization and cross-validation were applied in the ordinary least-squares linear regression in order to avoid over-fitting due to the multicollinearity of regressors, the results were compared against both the partial least-squares (PLS) regression and the un-regularized full-model regression. Nonparametric permutation testing scheme was applied to evaluate the statistical significance of regression. We found statistically significant correlation between the annotation model and 9 ICs out of 40 ICs. Regression analysis was also repeated for a large set of cubic ROIs covering the grey matter. Both IC- and ROI-based regression analyses revealed activations in parietal and occipital regions, with additional smaller clusters in the frontal lobe. Furthermore, we found elastic-net based regression more sensitive than PLS and un-regularized regression since it detected a larger number of significant ICs and ROIs. Along with the ISC ranking methods, our regression analysis proved a feasible method for ordering the ICs based on their functional relevance to the annotated cinematic features. The novelty of our method is - in comparison to the hypothesis-driven manual pre-selection and observation of some individual regressors biased by choice - in applying data-driven approach to all content features simultaneously. We found especially the combination of regularized regression and ICA useful when analyzing fMRI data obtained using non-narrative movie stimulus with a large set of complex and correlated features. (C) 2015 The Authors. Published by Elsevier Inc.Peer reviewe

Narrative comprehension beyond language : Common brain networks activated by a movie and its script

Narratives surround us in our everyday life in different forms. In the sensory brain areas, the processing of narratives is dependent on the media of presentation, be that in audiovisual or written form. However, little is known of the brain areas that process complex narrative content mediated by various forms. To isolate these regions, we looked for the functional networks reacting in a similar manner to the same narrative content despite different media of presentation. We collected 3-T fMRI whole brain data from 31 healthy human adults during two separate runs when they were either viewing a movie or reading its screenplay text. The independent component analysis (ICA) was used to separate 40 components. By correlating the components' time-courses between the two different media conditions, we could isolate 5 functional networks that particularly related to the same narrative content. These TOP-5 components with the highest correlation covered fronto-temporal, parietal, and occipital areas with no major involvement of primary visual or auditory cortices. Interestingly, the top-ranked network with highest modality-invariance also correlated negatively with the dialogue predictor, thus pinpointing that narrative comprehension entails processes that are not language-reliant. In summary, our novel experiment design provided new insight into narrative comprehension networks across modalities.Peer reviewe

Characteristics of the polymer transport in ratchet systems

Molecules with complex internal structure in time-dependent periodic potentials are studied by using short Rubinstein-Duke model polymers as an example. We extend our earlier work on transport in stochastically varying potentials to cover also deterministic potential switching mechanisms, energetic efficiency and non-uniform charge distributions. We also use currents in the non-equilibrium steady state to identify the dominating mechanisms that lead to polymer transportation and analyze the evolution of the macroscopic state (e.g., total and head-to-head lengths) of the polymers. Several numerical methods are used to solve the master equations and nonlinear optimization problems. The dominating transport mechanisms are found via graph optimization methods. The results show that small changes in the molecule structure and the environment variables can lead to large increases of the drift. The drift and the coherence can be amplified by using deterministic flashing potentials and customized polymer charge distributions. Identifying the dominating transport mechanism by graph analysis tools is found to give insight in how the molecule is transported by the ratchet effect.Comment: 35 pages, 17 figures, to appear in Phys. Rev.

Brain mechanisms underlying cue-based memorizing during free viewing of movie Memento

How does the human brain recall and connect relevant memories with unfolding events? To study this, we presented 25 healthy subjects, during functional magnetic resonance imaging, the movie 'Memento' (director C. Nolan). In this movie, scenes are presented in chronologically reverse order with certain scenes briefly overlapping previously presented scenes. Such overlapping "key-frames" serve as effective memory cues for the viewers, prompting recall of relevant memories of the previously seen scene and connecting them with the concurrent scene. We hypothesized that these repeating key-frames serve as immediate recall cues and would facilitate reconstruction of the story piece-by-piece. The chronological version of Memento, shown in a separate experiment for another group of subjects, served as a control condition. Using multivariate event-related pattern analysis method and representational similarity analysis, focal fingerprint patterns of hemodynamic activity were found to emerge during presentation of key-frame scenes. This effect was present in higher-order cortical network with regions including precuneus, angular gyrus, cingulate gyrus, as well as lateral, superior, and middle frontal gyri within frontal poles. This network was right hemispheric dominant. These distributed patterns of brain activity appear to underlie ability to recall relevant memories and connect them with ongoing events, i.e., "what goes with what" in a complex story. Given the real-life likeness of cinematic experience, these results provide new insight into how the human brain recalls, given proper cues, relevant memories to facilitate understanding and prediction of everyday life events.Peer reviewe

Processing of an Audiobook in the Human Brain Is Shaped by Cultural Family Background

Perception of the same narrative can vary between individuals depending on a listener’s previous experiences. We studied whether and how cultural family background may shape the processing of an audiobook in the human brain. During functional magnetic resonance imaging (fMRI), 48 healthy volunteers from two different cultural family backgrounds listened to an audiobook depicting the intercultural social life of young adults with the respective cultural backgrounds. Shared cultural family background increased inter-subject correlation of hemodynamic activity in the left-hemispheric Heschl’s gyrus, insula, superior temporal gyrus, lingual gyrus and middle temporal gyrus, in the right-hemispheric lateral occipital and posterior cingulate cortices as well as in the bilateral middle temporal gyrus, middle occipital gyrus and precuneus. Thus, cultural family background is reflected in multiple areas of speech processing in the brain and may also modulate visual imagery. After neuroimaging, the participants listened to the narrative again and, after each passage, produced a list of words that had been on their minds when they heard the audiobook during neuroimaging. Cultural family background was reflected as semantic differences in these word lists as quantified by a word2vec-generated semantic model. Our findings may depict enhanced mutual understanding between persons who share similar cultural family backgrounds

Single-layer metal-on-metal islands driven by strong time-dependent forces

Non-linear transport properties of single-layer metal-on-metal islands driven with strong static and time-dependent forces are studied. We apply a semi-empirical lattice model and use master equation and kinetic Monte Carlo simulation methods to compute observables such as the velocity and the diffusion coefficient. Two types of time-dependent driving are considered: a pulsed rotated field and an alternating field with a zero net force (electrophoretic ratchet). Small islands up to 12 atoms were studied in detail with the master equation method and larger ones with simulations. Results are presented mainly for a parametrization of Cu on Cu(001) surface, which has been the main system of interest in several previous studies. The main results are that the pulsed field can increase the current in both diagonal and axis direction when compared to static field, and there exists a current inversion in the electrophoretic ratchet. Both of these phenomena are a consequence of the coupling of the internal dynamics of the island with its transport. In addition to the previously discovered "magic size" effect for islands in equilibrium, a strong odd-even effect was found for islands driven far out of equilibrium. Master equation computations revealed non-monotonous behavior for the leading relaxation constant and effective Arrhenius parameters. Using cycle optimization methods, typical island transport mechanisms are identified for small islands.Comment: 39 pages, 20 figures, to appear in Phys. Rev. E [corrected typo of the x-axis label in Fig. 6

Processing of an Audiobook in the Human Brain Is Shaped by Cultural Family Background

Perception of the same narrative can vary between individuals depending on a listener’s previous experiences. We studied whether and how cultural family background may shape the processing of an audiobook in the human brain. During functional magnetic resonance imaging (fMRI), 48 healthy volunteers from two different cultural family backgrounds listened to an audiobook depicting the intercultural social life of young adults with the respective cultural backgrounds. Shared cultural family background increased inter-subject correlation of hemodynamic activity in the left-hemispheric Heschl’s gyrus, insula, superior temporal gyrus, lingual gyrus and middle temporal gyrus, in the right-hemispheric lateral occipital and posterior cingulate cortices as well as in the bilateral middle temporal gyrus, middle occipital gyrus and precuneus. Thus, cultural family background is reflected in multiple areas of speech processing in the brain and may also modulate visual imagery. After neuroimaging, the participants listened to the narrative again and, after each passage, produced a list of words that had been on their minds when they heard the audiobook during neuroimaging. Cultural family background was reflected as semantic differences in these word lists as quantified by a word2vec-generated semantic model. Our findings may depict enhanced mutual understanding between persons who share similar cultural family backgrounds

Vähemmän on enemmän : elliptinen kerronta dokumenttielokuvan leikkauksessa

KAUTTONEN, ANNIINA: Vähemmän on enemmän Elliptinen kerronta dokumenttielokuvan leikkauksessa Opinnäytetyö 55 sivua, joista liitteitä 12 sivua Marraskuu 2016 Elliptinen elokuvakerronta pitää sisällään tapahtumien tietoista poisjättämistä, tiedon viivyttelyä, avoimia lopetuksia, kaikkea sitä mitä ei elokuvassa syystä tai toisesta näytetä. Työn tavoitteena oli selvittää, millaisin keinoin elliptistä kerrontaa voidaan hyödyntää erityisesti dokumenttielokuvan leikkauksessa. Työn perusta oli lähdekirjallisuudessa ja referenssielokuvissa. Analysoitavaksi valittiin useita fiktio- ja dokumenttielokuvia, joissa ellipsiä on käytetty onnistuneesti. Tärkeiksi lähteiksi nousivat erityisesti elokuvaesteettikko Marcel Martinin tutkimuskirjallisuus sekä ranskalaisohjaaja Robert Bressonin elokuvat. Työssä esiteltiin prosessin aikana löydettyjä menetelmiä, jotka auttavat leikkaajaa hyödyntämään elliptistä kerrontaa. Näitä menetelmiä sovellettiin Lahja-työnimellä kulkevaan lyhyeen dokumenttielokuvaan, jota analysoitiin työn lopussa. Työn myötä löytyi useita konkreettisia elliptisen kerronnan keinoja. Elliptisyyden havaittiin näyttäytyvän useissa referenssielokuvissa oleellisena osana kerrontaa niin rakenteen kuin sisällönkin tasolla. Elliptisen kerronnan huomattiin osallistavan katsojansa onnistuneesti ja luovan näin mielenkiintoisempia ja vaikuttavampia tarinoita.KAUTTONEN, ANNIINA: Less Is More Elliptical Storytelling as a Part of Documentary Editing Bachelor's thesis 55 pages, appendices 12 pages November 2016 Elliptical storytelling in cinema includes conscious exclusion of story events, delaying of information, open endings and everything that is left out of the movie for some reason. The aim of this thesis was to find out how to utilize elliptical storytelling particularly in the editing of documentaries. The work’s basis lay in literary sources as well as movie references. It analysed several fiction and documentary films that have successfully used ellipsis in their storytelling. Theories found in the studies of film researcher Marcel Martin and films by the French director Robert Bresson were essential sources to this work. As a result, several methods were found that show how to utilize elliptical editing as part of the storytelling. These approaches were put to use in the planning of a short documentary that is presented and analyzed in the work. Several tools for elliptical storytelling were found as a result of the research. Ellipsis was found to be an essential part of storytelling in many of the analysed films both on a structural as well as contentual level. Elliptical storytelling engaged viewers successfully while making stories more interesting and effective