Periodically driven stochastic un- and refolding transitions of biopolymers

Mechanical single molecule experiments probe the energy profile of biomolecules. We show that in the case of a profile with two minima (like folded/unfolded) periodic driving leads to a stochastic resonance-like phenomenon. We demonstrate that the analysis of such data can be used to extract four basic parameters of such a transition and discuss the statistical requirements of the data acquisition. As advantages of the proposed scheme, a polymeric linker is explicitly included and thermal fluctuations within each well need not to be resolved.Comment: 7 pages, 5 figures, submitted to EP

Force induced stretched state: Effects of temperature

A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension (reaction co-ordinate) may increase or decrease with the temperature depending upon the applied force. The simple model developed here which incorporates semi-microscopic details of base direction provide an explanation of the force induced transitions in ssDNA as observed in experiments.Comment: 5 pages, 8 figures, RevTex

Reversible stretching of homopolymers and random heteropolymers

We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $\theta$-temperature is predicted to be sharp. For random sequences, however, the transition may be smoothed by a prevalence of necklace-like structures, in which globular regions and coil regions coexist in a single chain. As we show in the context of a random copolymer, preferential solvation of one monomer type lends stability to such structures. The range of stretching forces over which necklaces are stable is sensitive to chain length as well as sequence statistics.Comment: 14 pages, 4 figure

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

Rupture of multiple parallel molecular bonds under dynamic loading

Biological adhesion often involves several pairs of specific receptor-ligand molecules. Using rate equations, we study theoretically the rupture of such multiple parallel bonds under dynamic loading assisted by thermal activation. For a simple generic type of cooperativity, both the rupture time and force exhibit several different scaling regimes. The dependence of the rupture force on the number of bonds is predicted to be either linear, like a square root or logarithmic.Comment: 8 pages, 2 figure

A Quantitative Theory of Mechanical Unfolding of a Homopolymer Globule

We propose the quantitative mean-field theory of mechanical unfolding of a globule formed by long flexible homopolymer chain collapsed in poor solvent and subjected to extensional deformation. We demonstrate that depending on the degree of polymerization and solvent quality (quantified by the Flory-Huggins $\chi$ parameter) the mechanical unfolding of the collapsed chain may either occur continuously (by passing a sequence of uniformly elongated configurations) or involves intra-molecular micro-phase coexistence of a collapsed and a stretched segment followed by an abrupt unraveling transition. The force-extension curves are obtained and quantitatively compared to our recent results of numerical self-consistent field (SCF) simulations. The phase diagrams for extended homopolymer chains in poor solvent comprising one- and two-phase regions are calculated for different chain length or/and solvent quality.Comment: 24 pages, 18 figure

Thermal Fluctuations of Elastic Filaments with Spontaneous Curvature and Torsion

We study the effects of thermal flucutations on thin elastic filaments with spontaneous curvature and torsion. We derive analytical expressions for the orientational correlation functions and for the persistence length of helices, and find that this length varies non-monotonically with the strength of thermal fluctuations. In the weak fluctuation regime, the persistence length of a spontaneously twisted helix has three resonance peaks as a function of the twist rate. In the limit of strong fluctuations, all memory of the helical shape is lost.Comment: 1 figur

Clinical Psychology and the COVID-19 Pandemic: A Mixed Methods Survey Among Members of the European Association of Clinical Psychology and Psychological Treatment (EACLIPT)

Background: The COVID-19 pandemic has affected people globally both physically and psychologically. The increased demands for mental health interventions provided by clinical psychologists, psychotherapists and mental health care professionals, as well as the rapid change in work setting (e.g., from face-to-face to video therapy) has proven challenging. The current study investigates European clinical psychologists and psychotherapists' views on the changes and impact on mental health care that occurred due to the COVID-19 pandemic. It further aims to explore individual and organizational processes that assist clinical psychologists' and psychotherapists' in their new working conditions, and understand their needs and priorities. Method: Members of the European Association of Clinical Psychology and Psychological Treatment (EACLIPT) were invited (N = 698) to participate in a survey with closed and open questions covering their experiences during the first wave of the pandemic from June to September 2020. Participants (n = 92) from 19 European countries, mostly employed in universities or hospitals, completed the online survey. Results: Results of qualitative and quantitative analyses showed that clinical psychologists and psychotherapists throughout the first wave of the COVID-19 pandemic managed to continue to provide treatments for patients who were experiencing emotional distress. The challenges (e.g., maintaining a working relationship through video treatment) and opportunities (e.g., more flexibleflexibleflexibleworking hours) of working through this time were identified. Conclusions: Recommendations for mental health policies and professional organizations are identified, such as clear guidelines regarding data security and workshops on conducting video therapy