Translocation of a Single Stranded DNA Through a Conformationally Changing Nanopore

We investigate the translocation of a single stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times (FPT) of the translocation process is calculated, displaying a triple, double or mono peaked behavior, depending on the interconversion rates between the conformations, the applied electric field, and the initial conditions. The cumulative probability function of the FPT, in a field-free environment, is shown to have two regimes, characterized by fast and slow timescales. An analytical expression for the mean first passage time of the translocation process is derived, and provides, in addition to the interconversion rates, an extensive characterization of the translocation process. Relationships to experimental observations are discussed.Comment: 8 pages, 5 figures, Biophys. J., in pres

Single Stranded DNA Translocation Through A Nanopore: A Master Equation Approach

We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows that it can be either double or mono-peaked, depending on the system parameters. We show that the most probable translocation time is proportional to the polymer length, and inversely proportional to the first or second power of the voltage, depending on the initial conditions. The model recovers experimental observations on hetro-polymers when using their properties inside the pore, such as stiffness and polymer-pore interaction.Comment: 7 pages submitted to PR

99mTc-Besilesomab-SPECT/CT in Infectious Endocarditis: Upgrade of a Forgotten Method?

Infective endocarditis displays a serious condition with high mortality rates. Establishing a reliable diagnosis can be challenging. This study evaluates granulocyte imaging with 99mTc-Besilesomab-SPECT/CT in order to determine the clinical value of the method and its possible redefinition through the addition of hybrid imaging. The study comprises 26 consecutive patients with suspected infectious endocarditis or prosthetic valve infection that underwent 99mTc-Besilesomab-SPECT/CT in our facility between December 2016 and September 2018. 99mTc-Besilesomab-SPECT/CT images were reviewed by two independent and blinded observers and results were evaluated by transesophageal echocardiography (TEE) and blood culture results as well as by pathological, bacteriological, and clinical findings. Target-to-Background-Ratios were calculated for semi-quantitative analysis. 13/26 patients were in a post-surgical stage. 99mTc-Besilesomab-SPECT/CT was positive in 6 cases. All 6 cases were true positive confirmed by pathological or clinical findings according to the modified Duke Criteria for infective endocarditis. Remaining 19/26 cases were true negative. Target-to-Background ratios were significantly higher in patients that were visually scored positive compared to negative cases. Inter-observer agreement was very good of deciding whether a scan was positive or negative. Sensitivity of 99mTc-Besilesomab-SPECT/CT was 86–100% and specificity was 100%. 99mTc-Besilesomab-SPECT/CT is a useful imaging method for the diagnosis of endocarditis, especially in difficult cases with prosthetic valves or cardiac devices and inconclusive findings in echocardiography. The added value of SPECT/CT was mainly finding and localizing increased uptake at a certain valve, prosthesis, or device cable

Blinking statistics of a molecular beacon triggered by end-denaturation of DNA

We use a master equation approach based on the Poland-Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA, that is clamped at one end. In particular, we quantify the blinking dynamics of a fluorophore-quencher pair mounted within the denaturation wedge. We also study the behavioural changes in the presence of proteins, that selectively bind to single-stranded DNA. We show that such a setup could be well-suited as an easy-to-implement nanodevice for sensing environmental conditions in small volumes.Comment: 14 pages, 5 figures, LaTeX, IOP style. Accepted to J Phys Cond Mat special issue on diffusio

Representations for Three-Body T-Matrix on Unphysical Sheets: Proofs

A proof is given for the explicit representations which have been formulated in the author's previous work (nucl-th/9505028) for the Faddeev components of three-body T-matrix continued analytically on unphysical sheets of the energy Riemann surface. Also, the analogous representations for analytical continuation of the three-body scattering matrices and resolvent are proved. An algorithm to search for the three-body resonances on the base of the Faddeev differential equations is discussed.Comment: 98 Kb; LaTeX; Journal-ref was added (the title changed in the journal

Representations for Three-Body T-Matrix on Unphysical Sheets

Explicit representations are formulated for the Faddeev components of three-body T-matrix continued analytically on unphysical sheets of the energy Riemann surface. According to the representations, the T-matrix on unphysical sheets is obviously expressed in terms of its components taken on the physical sheet only. The representations for T-matrix are used then to construct similar representations for analytical continuation of three-body scattering matrices and resolvent. Domains on unphysical sheets are described where the representations obtained can be applied.Comment: 123 Kb; LaTeX; Journal-ref was added (the title changed in the journal

Translocation of structured polynucleotides through nanopores

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e., the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FEC's) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.Comment: 9 pages, 5 figure

Capillary filling with wall corrugations] Capillary filling in microchannels with wall corrugations: A comparative study of the Concus-Finn criterion by continuum, kinetic and atomistic approaches

We study the impact of wall corrugations in microchannels on the process of capillary filling by means of three broadly used methods - Computational Fluid Dynamics (CFD), Lattice-Boltzmann Equations (LBE) and Molecular Dynamics (MD). The numerical results of these approaches are compared and tested against the Concus-Finn (CF) criterion, which predicts pinning of the contact line at rectangular ridges perpendicular to flow for contact angles theta > 45. While for theta = 30, theta = 40 (no flow) and theta = 60 (flow) all methods are found to produce data consistent with the CF criterion, at theta = 50 the numerical experiments provide different results. Whilst pinning of the liquid front is observed both in the LB and CFD simulations, MD simulations show that molecular fluctuations allow front propagation even above the critical value predicted by the deterministic CF criterion, thereby introducing a sensitivity to the obstacle heigth.Comment: 25 pages, 8 figures, Langmuir in pres