The Role of Non-native Interactions in the Folding of Knotted Proteins

Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-acetylornithine carbamoyltransferase (AOTCase) and an unknotted ornithine carbamoyltransferase (OTCase). In addition, two different sets of pairwise amino acid interactions are considered: one promoting exclusively native interactions, and the other additionally including non-native quasi-chemical and electrostatic interactions. With the former model neither protein show a propensity to form knots. With the additional non-native interactions, knotting propensity remains negligible for the natively-unknotted OTCase while for AOTCase it is much enhanced. Analysis of the trajectories suggests that the different entanglement of the two transcarbamylases follows from the tendency of the C-terminal to point away from (for OTCase) or approach and eventually thread (for AOTCase) other regions of partly-folded protein. The analysis of the OTCase/AOTCase pair clarifies that natively-knotted proteins can spontaneously knot during early folding stages and that non-native sequence-dependent interactions are important for promoting and disfavoring early knotting events.Comment: Accepted for publication on PLOS Computational Biolog

Holographic field theory models of dark energy in interaction with dark matter

We discuss two lagrangian interacting dark energy models in the context of the holographic principle. The potentials of the interacting fields are constructed. The models are compared with CMB distance information, baryonic acoustic oscilations, lookback time and the Constitution supernovae sample. For both models the results are consistent with a non vanishing interaction between dark sectors - with more than three standard deviations of confidence for one of them. Moreover, in both cases, the sign of coupling is consistent with dark energy decaying into dark matter, alleviating the coincidence problem.Comment: arXiv admin note: substantial text overlap with arXiv:0912.399

Effect of Ring Rigidity on the Statics and Dynamics of Linear Catenanes

We used molecular dynamics simulations to investigate the statics and dynamics of poly[n]catenanes for different bending rigidities of the constituent rings. We show that stiffer rings yield catenanes with more extended and, at the same time, more flexible backbones. The softening of the backbone reflects the decreasing steric interactions of catenated rings as their shape becomes more oblate due to increased rigidity. The internal dynamics of catenanes is affected too. Going from flexible to rigid rings causes a several-fold slowing of different processes, from segmental rotations and size fluctuations to Rouse modes. Finally, by considering the statics and dynamics of crowded solutions of catenanes, we isolate another emergent property controlled by the rigidity of the rings. Specifically, we show that catenanes with rigid rings hinder each other's motion more than those with flexible rings. Thus, in equally crowded solutions, the diffusion coefficient is smaller for catenanes with stiffer rings

Linear Catenanes in Channel Confinement

We use Langevin dynamics simulations to investigate the behavior of linear catenanes under channel confinement. We consider model poly[n]catenanes of n = 100 rings, each of m = 40 beads, and present a comprehensive analysis of their statics and dynamics in cylindrical channels of various diameters. To highlight the impact of mechanical bonding, we compare the catenane behavior to an equivalent chain of beads under the same conditions. We show that linear catenanes exhibit various confinement regimes, including a de Gennes one for intermediate channel widths and an overstretching response for strong confinement, which is unique to catenanes. The catenane's relaxation dynamics also diverge from conventional polymers at strong confinement, presenting much slower modes. Through systematic analysis of the size, shape, and orientation of the concatenated rings and their mechanical bonds, we shed light on the underlying mechanisms driving the catenane's static and dynamic responses to confinement

Depletion effects and loop formation in self-avoiding polymers

Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the enhanced viscous friction. For short chains, the enhanced friction slows down looping, while, for longer chains, the depletion attraction renders it more frequent and persistent. We discuss the possible relevance of the findings for chromatin looping in living cells.Comment: 4 pages, 3 figure

Polymer Physics by Quantum Computing

Sampling equilibrium ensembles of dense polymer mixtures is a paradigmatically hard problem in computational physics, even in lattice-based models. Here, we develop a formalism based on interacting binary tensors that allows for tackling this problem using quantum annealing machines. Our approach is general in that properties such as self-Avoidance, branching, and looping can all be specified in terms of quadratic interactions of the tensors. Microstates' realizations of different lattice polymer ensembles are then seamlessly generated by solving suitable discrete energy-minimization problems. This approach enables us to capitalize on the strengths of quantum annealing machines, as we demonstrate by sampling polymer mixtures from low to high densities, using the D-Wave quantum annealer. Our systematic approach offers a promising avenue to harness the rapid development of quantum machines for sampling discrete models of filamentous soft-matter systems

Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle

A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from chemical propensity to simple geometrical reasoning have been invoked to rationalize the existence of such secondary structures. We formulate a dynamical variational principle for selection in conformation space based on the requirement that the backbone of the native state of biologically viable polymers be rapidly accessible from the denatured state. The variational principle is shown to result in the emergence of helical order in compact structures.Comment: 4 pages, RevTex, 4 eps figure

Origin of atmospheric aerosols at the Pierre Auger Observatory using backward trajectory of air masses

The Pierre Auger Observatory is the largest operating cosmic ray observatory ever built. Calorimetric measurements of extensive air showers induced by cosmic rays are performed with a fluorescence detector. Thus, one of the main challenges is the monitoring of the atmosphere, both in terms of atmospheric state variables and optical properties. To better understand the atmospheric conditions, a study of air mass trajectories above the site is presented. Such a study has been done using an air-modelling program well known in atmospheric sciences. Its validity has been checked using meteorological radiosonde soundings performed at the Pierre Auger Observatory. Finally, aerosol concentration values measured by the Central Laser Facility are compared to backward trajectories.Comment: 4 pages, 6 figures -- ECRS'12 European Cosmic Ray Symposium (July, 3-7, 2012) at Moscow, Russi

RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration

We use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide-long xrRNA from the Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on time scales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, for both activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings provide a useful reference to interpret and design future theoretical and experimental studies of RNA translocation

A complete devil's staircase in the Falicov-Kimball model

We consider the neutral, one-dimensional Falicov-Kimball model at zero temperature in the limit of a large electron--ion attractive potential, U. By calculating the general n-ion interaction terms to leading order in 1/U we argue that the ground-state of the model exhibits the behavior of a complete devil's staircase.Comment: 6 pages, RevTeX, 3 Postscript figure