Confinement induces helical organization of chromosome-like polymers

Hi-C-guided many-polymer model to decipher 3D genome organization

We propose a high-throughput chromosome conformation capture data-based many-polymer model that allows us to generate an ensemble of multi-scale genome structures. We demonstrate the efficacy of our model by validating the generated structures against experimental measurements and employ them to address key questions regarding genome organization. Our model first confirms a significant correlation between chromosome size and nuclear positioning. Specifically, smaller chromosomes are distributed at the core region, whereas larger chromosomes are at the periphery, interacting with the nuclear envelope. The spatial distribution of A- and B-type compartments, which is nontrivial to infer from the corresponding high-throughput chromosome conformation capture maps alone, can also be elucidated using our model, accounting for an issue such as the effect of chromatin-lamina interaction on the compartmentalization of conventional and inverted nuclei. In accordance with imaging data, the overall shape of the 3D genome structures generated from our model displays significant variation. As a case study, we apply our method to the yellow fever mosquito genome, finding that the predicted morphology displays, on average, a more globular shape than the previously suggested spindle-like organization and that our prediction better aligns with the fluorescence in situ hybridization data. Our model has great potential to be extended to investigate many outstanding issues concerning 3D genome organization.

DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling

DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation. Highlighted in vitro and in vivo in the 1960s and 1970s, respectively, the first physical models were proposed concomitantly in order to predict the deformation properties of the double helix. About fifteen years later, polymer physics models demonstrated on larger scales the plectonemic nature and the tree-like organization of supercoiled DNA. Since then, many works have tried to establish a better understanding of the multiple structuring and physiological properties of bacterial DNA in thermodynamic equilibrium and far from equilibrium. The purpose of this essay is to address upcoming challenges by thoroughly exploring the relevance, predictive capacity, and limitations of current physical models, with a specific focus on structural properties beyond the scale of the double helix. We discuss more particularly the problem of DNA conformations, the interplay between DNA supercoiling with gene transcription and DNA replication, its role on nucleoid formation and, finally, the problem of scaling up models. Our primary objective is to foster increased collaboration between physicists and biologists. To achieve this, we have reduced the respective jargon to a minimum and we provide some explanatory background material for the two communities.

Knot Formation on DNA Pushed Inside Chiral Nanochannels

We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels.

Shock compression of semiflexible polymers

We employ molecular dynamics simulations to investigate the shock compression of linear semiflexible polymers. While the propagation velocity of a shock primarily depends on density, both chain rigidity and chain orientation significantly influence the shock width and the final temperature of the system. In general, the shock wave triggers molecular buckling in chains oriented perpendicular to the compression front. Following the passage of the front, the semiflexible chains buckle with a wavelength that decreases with the compression speed as λm ∼ up-0.2, and subsequent relaxation leads to a banana-like liquid crystal phase. In ordered systems with molecules oriented perpendicular to the compression front, the shock width increases by a factor of up to 10 compared to a similar isotropic system, resulting in enhanced shock energy absorption. These findings indicate that chain stiffness plays a critical role in the impact absorption properties of polymeric materials.

Knot Factories with Helical Geometry Enhance Knotting and Induce Handedness to Knots

We performed molecular dynamics simulations of DNA polymer chains confined in helical nano-channels under compression in order to explore the potential of knot-factories with helical geometry to produce knots with a preferred handedness. In our simulations, we explore mutual effect of the confinement strength and compressive forces in a range covering weak, intermediate and strong confinement together with weak and strong compressive forces. The results find that while the common metrics of polymer chain in cylindrical and helical channels are very similar, the DNA in helical channels exhibits greatly different topology in terms of chain knottedness, writhe and handedness of knots. The results show that knots with a preferred chirality in terms of average writhe can be produced by using channels with a chosen handedness.

A New Conceptual 'Cylinder' Framework for Sustainable Bioeconomy Systems and Their Actors

Concepts for sustainable bioeconomy systems are gradually replacing the ones on linear product chains. The reason is that continuously expanding linear chain activities are considered to contribute to climate change, reduced biodiversity, over-exploitation of resources, food insecurity, and the double burden of disease. Are sustainable bioeconomy systems a guarantee for a healthy planet? If yes, why, when, and how? In literature, different sustainability indicators have been presented to shed light on this complicated question. Due to high degrees of complexity and interactions of actors in bioeconomy systems, trade-offs and non-linear outcomes became apparent. This fueled the debates about the normative dimensions of the bioeconomy. In particular, the behavior of actors and the utilization of products do not seem to be harmonized according to the environmental, social, and economic pillars of sustainability. Potential conflicts require a new conceptual framework that is here introduced. It consists of a 'sustainability' cylinder captured between an inner-cylinder, representing order, and an outer-cylinder for chaos, based on the laws of physics and complex adaptive systems. Such a framework permits (bioeconomy) systems to propagate in the sustainability zone only if they follow helical pathways serving as the new norms. Helices are a combination of two sinusoidal patterns. The first represents here the sustainable behavior of interacting actors and the second the balanced usage of resources and products. The latter counteracts current growth discourses. The applicability of the conceptual cylinder framework is positively verified via 9 cases in Europe, which encompass social-organizational and product-technological innovations.

Conformational transitions and helical structures of a dipolar chain in external electric fields

The conformational behavior of a single dipolar chain in a uniform electric field is investigated by molecular dynamics simulations. The dipolar chain is modeled as a backbone bead-on-spring chain of equally charged beads, each connected by a rigid spring with an oppositely charged side bead that can freely rotate around the backbone bead. In the strong coupling regime, when the dipolar chain is in the globular state due to a strong electrostatic correlational attraction, the application of an electric field causes the chain swelling and elongation along the field direction. In the weak coupling regime, a qualitatively new regime is found when the swollen dipolar chain shrinks along the field direction adopting flattened conformations due to the field-induced anisotropy of the chain rigidity and the head-to-tail attraction of the dipoles orienting along the field lines. A novel helical conformation is detected for low-polar media and strong electric fields. An increasing rigidity of the backbone chain leads to some stabilization of the helical conformation and the formation of double and triple helices as well as flat spread springs. Fine tuning of the interplay between dipolar and volume interactions by external electric fields induces re-orientation of rod-like dipolar chains in dilute solutions. The obtained results can provide new ways to control dipolar polymer conformations and design materials with responsive properties.

Silylium cation initiated sergeants-and-soldiers type chiral amplification of helical aryl isocyanide copolymers

Silylium cations act as new highly efficient metal-free single-component cationic initiators for the cationic polymerization and copolymerization of chiral or achiral aryl isocyanides, preparing optically active polymers and copolymers obeying “sergeants-and-soldiers” rule.

Mechanical property of the helical configuration for a twisted intrinsically straight biopolymer

We explore the effects of two typical torques on the mechanical property of the helical configuration for an intrinsically straight filament or biopolymer either in three-dimensional space or on a cylinder. One torque is parallel to the direction of a uniaxial applied force, and is coupled to the cross section of the filament. We obtain some algebraic equations for the helical configuration and find that the boundary conditions are crucial. In three-dimensional space, we show that the extension is always a monotonic function of the applied force. On the other hand, for a filament confined on a cylinder, the twisting rigidity and torque coupled to the cross section are irrelevant in forming a helix if the filament is isotropic and under free boundary condition. However, the twisting rigidity and the torque coupled to the cross section become crucial when the Euler angle at two ends of the filament are fixed. Particularly, the extension of a helix can subject to a first-order transition so that in such a condition a biopolymer can act as a switch or sensor in some biological processes. We also present several phase diagrams to provide the conditions to form a helix.