scholarly journals Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids

2021 ◽  
Vol 7 (20) ◽  
pp. eabf9260
Author(s):  
Jan Smrek ◽  
Jonathan Garamella ◽  
Rae Robertson-Anderson ◽  
Davide Michieletto
Keyword(s):  
Large Scale ◽  
Theoretical Models ◽  
Polymer Physics ◽  
Natural Occurrence ◽  
Fundamental Physics ◽  
Supercoiled Dna ◽  
Dna Mobility ◽  
Topological States ◽  
Ring Polymers ◽  
Dynamics Simulations

Ring polymers in dense solutions are among the most intriguing problems in polymer physics. Because of its natural occurrence in circular form, DNA has been extensively used as a proxy to study the fundamental physics of ring polymers in different topological states. Yet, torsionally constrained—such as supercoiled—topologies have been largely neglected so far. The applicability of existing theoretical models to dense supercoiled DNA is thus unknown. Here, we address this gap by coupling large-scale molecular dynamics simulations with differential dynamic microscopy of entangled supercoiled DNA plasmids. We find that, unexpectedly, larger supercoiling increases the size of entangled plasmids and concomitantly induces an enhancement in DNA mobility. These findings are reconciled as due to supercoiling-driven asymmetric and double-folded plasmid conformations that reduce interplasmid entanglements and threadings. Our results suggest a way to topologically tune DNA mobility via supercoiling, thus enabling topological control over the (micro)rheology of DNA-based complex fluids.

scholarly journals Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking

2018 ◽  
Author(s):  
Lucia Coronel ◽  
Antonio Suma ◽  
Cristian Micheletti
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Conformational Ensemble ◽  
Supercoiled Dna ◽  
Cooperative Action ◽  
Bacterial Plasmids ◽  
Catalytic Processes ◽  
Dna Strand ◽  
Dynamics Simulations

AbstractKnots and supercoiling are both introduced in bacterial plasmids by catalytic processes involving DNA strand passages. While the effects on plasmid organization has been extensively studied for knotting and supercoiling taken separately, much less is known about their concurrent action. Here, we use molecular dynamics simulations and oxDNA, an accurate mesoscopic DNA model, to study the kinetic and metric changes introduced by complex (five-crossing) knots and supercoiling in 2kbp-long DNA rings. We find several unexpected results. First, the conformational ensemble is dominated by two distinct states, differing in branchedness and knot size. Secondly, fluctuations between these states are as fast as the metric relaxation of unknotted rings. In spite of this, certain boundaries of knotted and plectonemically-wound regions can persist over much longer timescales. These pinned regions involve multiple strands that are interlocked by the cooperative action of topological and supercoiling constraints. Their long-lived character may be relevant for the simplifying action of topoisomerases.

scholarly journals Ionic Screening in Bulk and under Confinement

2021 ◽  
Author(s):  
Johannes Zeman ◽  
Svyatoslav Kondrat ◽  
Christian Holm
Keyword(s):  
Ionic Liquids ◽  
Large Scale ◽  
Theoretical Models ◽  
Quantitative Agreement ◽  
Decay Length ◽  
Confined Systems ◽  
Ionic Systems ◽  
Concentrated Electrolytes ◽  
High Concentrations ◽  
Dynamics Simulations

Recent experiments have shown that the repulsive force between atomically flat, like-charged surfaces confining room-temperature ionic liquids or concentrated electrolytes exhibits an anomalously large decay length. In our previous publication [Zeman et al., Chem. Commun. 56, 15635 (2020)], we showed by means of extremely large-scale molecular dynamics simulations that this so-called underscreening effect might not be a feature of bulk electrolytes. Herein, we corroborate these findings by providing additional results with more detailed analyses and expand our investigations to ionic liquids under confinement. Unlike in bulk systems, where screening lengths are computed from the decay of interionic potentials of mean force (PMFs), we extract such data in confined systems from cumulative charge distributions. At high concentrations, our simulations show increasing screening lengths with increasing electrolyte concentration, consistent with classical liquid state theories. However, our analyses demonstrate that---also for confined systems---there is no anomalously large screening length. As expected, the screening lengths determined for ionic liquids under confinement are in good quantitative agreement with the screening lengths of the same ionic systems in bulk. In addition, we show that some theoretical models used in the literature to relate the measured screening lengths to other observables are inapplicable to highly concentrated electrolytes.

scholarly journals Supercoiling Enhances DNA Mobility by Reducing Threadings and Entanglements

2020 ◽  
Author(s):  
Jan Smrek ◽  
Davide Michieletto
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Md Simulations ◽  
Supercoiled Dna ◽  
Dna Mobility ◽  
Average Size ◽  
Open Question ◽  
Entangled Solutions

DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained – or supercoiled – DNA plasmids are largely neglected; this is partly due to the limited understanding of how supercoiling affects the rheology of entangled DNA. To address this open question we perform large scale Molecular Dynamics (MD) simulations of entangled solutions of DNA plasmids modelled as twistable chains. We discover that, contrarily to what generally assumed in the literature, larger supercoiling increases the average size of plasmids in the entangled regime. At the same time, we discover that this is accompanied by an unexpected increase of diffusivity. We explain our findings as due to a decrease in inter-plasmids threadings and entanglements.

Opinion Dynamics Optimization by Varying Susceptibility to Persuasion via Non-Convex Local Search

2021 ◽  
Vol 16 (2) ◽  
pp. 1-34
Author(s):  
Rediet Abebe ◽  
T.-H. HUBERT Chan ◽  
Jon Kleinberg ◽  
Zhibin Liang ◽  
David Parkes ◽  
...  
Keyword(s):  
Local Search ◽  
Objective Function ◽  
Iterative Process ◽  
Large Scale ◽  
Opinion Dynamics ◽  
Theoretical Models ◽  
Global Optimum ◽  
Local Optimum ◽  
Opinion Formation ◽  
Long Line

A long line of work in social psychology has studied variations in people’s susceptibility to persuasion—the extent to which they are willing to modify their opinions on a topic. This body of literature suggests an interesting perspective on theoretical models of opinion formation by interacting parties in a network: in addition to considering interventions that directly modify people’s intrinsic opinions, it is also natural to consider interventions that modify people’s susceptibility to persuasion. In this work, motivated by this fact, we propose an influence optimization problem. Specifically, we adopt a popular model for social opinion dynamics, where each agent has some fixed innate opinion, and a resistance that measures the importance it places on its innate opinion; agents influence one another’s opinions through an iterative process. Under certain conditions, this iterative process converges to some equilibrium opinion vector. For the unbudgeted variant of the problem, the goal is to modify the resistance of any number of agents (within some given range) such that the sum of the equilibrium opinions is minimized; for the budgeted variant, in addition the algorithm is given upfront a restriction on the number of agents whose resistance may be modified. We prove that the objective function is in general non-convex. Hence, formulating the problem as a convex program as in an early version of this work (Abebe et al., KDD’18) might have potential correctness issues. We instead analyze the structure of the objective function, and show that any local optimum is also a global optimum, which is somehow surprising as the objective function might not be convex. Furthermore, we combine the iterative process and the local search paradigm to design very efficient algorithms that can solve the unbudgeted variant of the problem optimally on large-scale graphs containing millions of nodes. Finally, we propose and evaluate experimentally a family of heuristics for the budgeted variant of the problem.

scholarly journals Elucidating the Onset of Plasticity in Sliding Contacts Using Differential Computational Orientation Tomography

2021 ◽  
Vol 69 (3) ◽  
Author(s):  
S. J. Eder ◽  
P. G. Grützmacher ◽  
M. Rodríguez Ripoll ◽  
J. F. Belak
Keyword(s):  
Grain Boundary ◽  
Large Scale ◽  
Surface Deformation ◽  
Boundary Migration ◽  
Material Design ◽  
Lattice Rotation ◽  
Time Resolved ◽  
Near Surface ◽  
Color Saturation ◽  
Dynamics Simulations

Abstract Depending on the mechanical and thermal energy introduced to a dry sliding interface, the near-surface regions of the mated bodies may undergo plastic deformation. In this work, we use large-scale molecular dynamics simulations to generate “differential computational orientation tomographs” (dCOT) and thus highlight changes to the microstructure near tribological FCC alloy surfaces, allowing us to detect subtle differences in lattice orientation and small distances in grain boundary migration. The analysis approach compares computationally generated orientation tomographs with their undeformed counterparts via a simple image analysis filter. We use our visualization method to discuss the acting microstructural mechanisms in a load- and time-resolved fashion, focusing on sliding conditions that lead to twinning, partial lattice rotation, and grain boundary-dominated processes. Extracting and laterally averaging the color saturation value of the generated tomographs allows us to produce quantitative time- and depth-resolved maps that give a good overview of the progress and severity of near-surface deformation. Corresponding maps of the lateral standard deviation in the color saturation show evidence of homogenization processes occurring in the tribologically loaded microstructure, frequently leading to the formation of a well-defined separation between deformed and undeformed regions. When integrated into a computational materials engineering framework, our approach could help optimize material design for tribological and other deformation problems. Graphic Abstract .

scholarly journals Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth

2016 ◽  
Vol 34 (4) ◽  
pp. 041509 ◽  
Author(s):  
Daniel Edström ◽  
Davide G. Sangiovanni ◽  
Lars Hultman ◽  
Ivan Petrov ◽  
J. E. Greene ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Epitaxial Film ◽  
Film Growth ◽  
Dynamics Simulations ◽  
Epitaxial Film Growth

Creep of frozen slopes and ice-filled rock joints under temperature variation

2006 ◽  
Vol 33 (6) ◽  
pp. 719-725 ◽  
Author(s):  
Branko Ladanyi
Keyword(s):  
Creep Behavior ◽  
Large Scale ◽  
Variable Temperature ◽  
Theoretical Models ◽  
Rock Joints ◽  
Interface Problems ◽  
Frozen Ground ◽  
Rock Glaciers ◽  
Rock Interface ◽  
Creep Temperature

Owing to climate warming trends, there has been an increasing interest in recent years in the accelerating creep of rock glaciers and frozen slopes. In the field of glaciology, the creep of glaciers has been extensively studied, observed, and analyzed for more than 100 years. Many valuable and detailed theoretical models have been proposed through the years for simulating the creep behavior of glaciers. This synthesis paper has no intention of proposing another one. Its purpose is only to supply to these models a potential geotechnical background, borrowed from the connected fields of frozen ground mechanics, rock mechanics, and the mechanics of mixtures. In particular, this paper attempts to extend some known models of mechanical behavior of unfrozen soil and rock masses to masses containing ice and to apply these models to large-scale creep of ice–rock mixtures and ice–rock interface problems under variable temperature and stress conditions.Key words: ice, rock, mixture, rock joints, slope stability, creep, temperature.

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