Structure and Microrheology of Complex Polymer Solutions: from Genome Organization to Active-Passive Mixtures

Polymers are intriguing physical systems whose complex properties are at the heart of how viscoelastic substances, materials which under strain manifest a behavior which is intermediate between a liquid and a solid, work. Understanding the properties of these materials is the main goal of the theoretical and computational tools of Polymer Physics. A particularly important, yet not fully understood, class of polymer materials is represented by concentrated solutions and melts of unknotted and unconcatenated ring polymers: in fact, at odds with the more familiar case of linear polymers which tend to become highly mixed and mutually penetrating, the presence of mutual avoidance and topological constraints (entanglements) between ring polymers force these chains to remain \u201cterritorial\u201d, i.e. each chain is virtually unmixed from the rest of the others. Because of this feature, solutions of ring polymers display unique material properties, in particular single chains tend to crumple into highly branched conformations and feature marked corrugated surfaces. Recently, it has been suggested that the spatial configurations of ring polymers in solution can be used as model systems for the organization of chromosome conformations during interphase, i.e. inside the nuclei of eukaryotic cells. This surprising analogy is built upon the claim that chromosomes undergo slow relaxation inside the nucleus which results in the spontaneous formation of so-called territories, regions of the nucleus which have a profound impact on crucial cellular functions such as gene expression and gene regulation. In this Thesis, we explore the analogy between ring polymers in solution, their large-scale crumpled 3d structure and interphase chromosomes by employing a combination of the theory of polymer solutions and numerical simulations. In more detail, we investigate primarily the following aspects: (a) the formation of ordered domains on a simple Ising-like toy model for crumpled polymers; (b) The analysis of the viscoelastic properties of model chromosome conformations whose stochastic motion is restricted by the presence of external constraints; (c) The discussion of the viscoelastic properties of solutions of active vs. non- active rings, where \u201dactive\u201d means that polymers are driven out-of-equilibrium by pumping energy inside the system

Structure and microrheology of genome organization: From experiments to physical modeling.

The mechanisms beyond chromosome folding within the nuclei of eukaryotic cells have fundamental implications in important processes like gene expression and regulation. Yet, they remain widely unknown. Unveiling the secrets of nuclear processes requires a cross-disciplinary approach combining experimental techniques to theoretical, mathematical and physical modeling. In this review, we discuss our current understanding of the generic aspects of genome organization during interphase in terms of the conceptual connection between the large-scale structure of chromosomes and the physics beyond the crumpled structure of entangled ring polymers in solution. Then, we employ this framework to discuss recent experimental and theoretical results for microrheology of Brownian nanoprobes dispersed in the nuclear medium

Foreground Enhancement and Background Suppression in Human Early Visual System During Passive Perception of Natural Images

One of the major challenges in visual neuroscience is represented by foreground-background segmentation, a process that is supposed to rely on computations in cortical modules, as information progresses from V1 to V4. Data from nonhuman primates (Poort et al., 2016) showed that segmentation leads to two distinct, but associated processes: the enhancement of cortical activity associated to figure processing (i.e., foreground enhancement) and the suppression of ground-related cortical activity (i.e., background suppression). To characterize foreground-background segmentation of natural stimuli in humans, we parametrically modulated low-level properties of 334 images and their behaviorally segmented counterparts. A model based on simple visual features was then adopted to describe the filtered and intact images, and to evaluate their resemblance with fMRI activity in different visual cortices (V1, V2, V3, V3A, V3B, V4, LOC). Results from representational similarity analysis (Kriegeskorte et al., 2008) showed that the correspondence between behaviorally segmented natural images and brain activity increases throughout the visual processing stream. We found evidence of foreground enhancement for all the tested visual regions, while background suppression occurs in V3B, V4 and LOC. Our results suggest that foreground-background segmentation is an automatic process that occurs during natural viewing, and cannot be merely ascribed to differences in objects size or location. Finally, neural images reconstructed from V4 and LOC fMRI activity revealed a preserved spatial resolution of foreground textures, indicating a richer representation of the salient part of natural images, rather than a simplistic model of objects shape

modality independent encoding of individual concepts in the left parietal cortex

Abstract The organization of semantic information in the brain has been mainly explored through category-based models, on the assumption that categories broadly reflect the organization of conceptual knowledge. However, the analysis of concepts as individual entities, rather than as items belonging to distinct superordinate categories, may represent a significant advancement in the comprehension of how conceptual knowledge is encoded in the human brain. Here, we studied the individual representation of thirty concrete nouns from six different categories, across different sensory modalities (i.e., auditory and visual) and groups (i.e., sighted and congenitally blind individuals) in a core hub of the semantic network, the left angular gyrus, and in its neighboring regions within the lateral parietal cortex. Four models based on either perceptual or semantic features at different levels of complexity (i.e., low- or high-level) were used to predict fMRI brain activity using representational similarity encoding analysis. When controlling for the superordinate component, high-level models based on semantic and shape information led to significant encoding accuracies in the intraparietal sulcus only. This region is involved in feature binding and combination of concepts across multiple sensory modalities, suggesting its role in high-level representation of conceptual knowledge. Moreover, when the information regarding superordinate categories is retained, a large extent of parietal cortex is engaged. This result indicates the need to control for the coarse-level categorial organization when performing studies on higher-level processes related to the retrieval of semantic information

Assessment of full carbon budget of Italy: the CarbIUS project

Regional carbon balances, funded, for the Italian side, by the Italian Ministry of Environment in the context of a bilateral agreement to develop scientific collaborations in Global Change Research between Italy and USA signed in 2001. The two regions selected are Italy and Oregon-California; there are many similarities between these two regions (climate, vegetation, topography, population pressure, etc.) but, on other hand, there are also interesting contrasts in societal aspects like demography, land-use history and emissions. The main CarbIUS objectives are 1) the identification of spatial and temporal variability of carbon sources and sinks and the relative contribution of the different anthropogenic and biogenic components, 2) the impact of land use changes and human population dynamics on the carbon balance, 3) the quantification of the effects of climate and natural disturbances on the terrestrial carbon stocks and fluxes and 4) the application of new methodologies to investigate carbon metabolism at the plot, ecosystem and regional scale. In this paper will be presented the methodologies that we are using to assess the contribution of the different components to the full carbon budget, like carbon stocks and fluxes, disturbances (harvesting, wild forest fires and forest pathology), CH4 and NO2 fluxes and anthropogenic emissions. All these information will be input in a Data Assimilation System and the results will be validated using sub-regional airborne measurements of carbon fluxes