Theory of biopolymer stretching at high forces

We provide a unified theory for the high force elasticity of biopolymers solely in terms of the persistence length, $\xi_p$, and the monomer spacing, $a$. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the Worm-like Chain (WLC) is a better model. We show that $\xi_p$ can be estimated from the force extension curve (FEC) at the extension $x\approx 1/2$ (normalized by the contour length of the biopolymer). After validating the theory using simulations, we provide a quantitative analysis of the FECs for a diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and unstructured PEVK domain of titin) for $x \ge 1/2$. The success of a specific polymer model (FJC or WLC) to describe the FEC of a given biopolymer is naturally explained by the theory. Only by probing the response of biopolymers over a wide range of forces can the $f$-dependent elasticity be fully described.Comment: 20 pages, 4 figure

Ocean warming drives rapid dynamic activation of a marine-terminating glacier on the west Antarctic Peninsula

Ice dynamic change is the primary cause of mass loss from the Antarctic Ice Sheet, thus it is important to understand the processes driving ice-ocean interactions and the timescale on which major change can occur. Here we use satellite observations to measure a rapid increase in speed and collapse of the ice shelf fronting Cadman Glacier in the absence of surface meltwater ponding. Between November 2018 and December 2019 ice speed increased by 94 ± 4% (1.47 ± 0.6 km/yr), ice discharge increased by 0.52 ± 0.21 Gt/yr, and the calving front retreated by 8 km with dynamic thinning on grounded ice of 20.1 ± 2.6 m/yr. This change was concurrent with a positive temperature anomaly in the upper ocean, where a 400 m deep channel allowed warm water to reach Cadman Glacier driving the dynamic activation, while neighbouring Funk and Lever Glaciers were protected by bathymetric sills across their fjords. Our results show that forcing by warm ocean water can cause the rapid onset of dynamic imbalance and increased ice discharge from glaciers on the Antarctic Peninsula, highlighting the region’s sensitivity to future climate variability

Error sources and guidelines for quality assessment of glacier area, elevation change, and velocity products derived from satellite data in the Glaciers_cci project

Satellite data provide a large range of information on glacier dynamics and changes. Results are often reported, provided and used without consideration of measurement accuracy (difference to a true value) and precision (variability of independent assessments). Whereas accuracy might be difficult to determine due to the limited availability of appropriate reference data and the complimentary nature of satellite measurements, precision can be obtained from a large range of measures with a variable effort for determination. This study provides a systematic overview on the factors influencing accuracy and precision of glacier area, elevation change (from altimetry and DEM differencing), and velocity products derived from satellite data, along with measures for calculating them. A tiered list of recommendations is provided (sorted for effort from Level 0 to 3) as a guide for analysts to apply what is possible given the datasets used and available to them. The more simple measures to describe product quality (Levels 0 and 1) can often easily be applied and should thus always be reported. Medium efforts (Level 2) require additional work but provide a more realistic assessment of product precision. Real accuracy assessment (Level 3) requires independent and coincidently acquired reference data with high accuracy. However, these are rarely available and their transformation into an unbiased source of information is challenging. This overview is based on the experiences and lessons learned in the ESA project Glaciers_cci rather than a review of the literature

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Widespread increase in dynamic imbalance in the Getz region of Antarctica from 1994 to 2018

The Getz region of West Antarctica is losing ice at an increasing rate; however, the forcing mechanisms remain unclear. Here we use satellite observations and an ice sheet model to measure the change in ice speed and mass balance of the drainage basin over the last 25-years. Our results show a mean increase in speed of 23.8 % between 1994 and 2018, with three glaciers accelerating by over 44 %. Speedup across the Getz basin is linear, with speedup and thinning directly correlated confirming the presence of dynamic imbalance. Since 1994, 315 Gt of ice has been lost contributing 0.9 ± 0.6 mm global mean sea level, with increased loss since 2010 caused by a snowfall reduction. Overall, dynamic imbalance accounts for two thirds of the mass loss from this region of West Antarctica over the past 25-years, with a longer-term response to ocean forcing the likely driving mechanism

Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms

The main functions of viral capsids are to protect, transport and deliver their genome. The mechanical properties of capsids are supposed to be adapted to these tasks. Bacteriophage capsids also need to withstand the high pressures the DNA is exerting onto it as a result of the DNA packaging and its consequent confinement within the capsid. It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. DNA packaging and ejection strategies are obviously dependent on the mechanical properties of the capsid. This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular

DNA primase acts as a molecular brake in DNA replication

A hallmark feature of DNA replication is the coordination between the continuous polymerization of nucleotides on the leading strand and the discontinuous synthesis of DNA on the lagging strand. This synchronization requires a precisely timed series of enzymatic steps that control the synthesis of an RNA primer, the recycling of the lagging-strand DNA polymerase, and the production of an Okazaki fragment. Primases synthesize RNA primers at a rate that is orders of magnitude lower than the rate of DNA synthesis by the DNA polymerases at the fork. Furthermore, the recycling of the lagging-strand DNA polymerase from a finished Okazaki fragment to a new primer is inherently slower than the rate of nucleotide polymerization. Different models have been put forward to explain how these slow enzymatic steps can take place at the lagging strand without losing coordination with the continuous and fast leading-strand synthesis. Nonetheless, a clear picture remains elusive. Here we use single-molecule techniques to study the kinetics of a multiprotein replication complex from bacteriophage T7 and to characterize the effect of primase activity on fork progression. We observe the synthesis of primers on the lagging strand to cause transient pausing of the highly processive leading-strand synthesis. In the presence of both leading- and lagging-strand synthesis, we observe the formation and release of a replication loop on the lagging strand. Before loop formation, the primase acts as a molecular brake and transiently halts progression of the replication fork. This observation suggests a mechanism that prevents leading-strand synthesis from outpacing lagging-strand synthesis during the slow enzymatic steps on the lagging strand