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

Predicting Caries by Measuring Its Activity Using Quantitative Light-Induced Fluorescence in vivo: A 2-Year Caries Increment Analysis

The aim of this study was to analyse the predictive power of several clinical baseline parameters and the de-/remineralisation properties of in vivo etched sites measured with quantitative light-induced fluorescence (QLF) for subsequent 2-year caries increment. At baseline, in 44 children (8.23 ± 1.5 years) two areas (diameter 2 mm) of the buccal surface of a primary posterior tooth were etched with 36% phosphoric acid gel for 1 and 4 min, respectively. The etched sites were analysed immediately after etching (ΔQ1) and 24 h (ΔQ2) later by QLF. Additionally, caries status (deft/DMFT and initial caries), approximal plaque, bleeding on probing, and the patient’s current use of fluorides were recorded. In the 2-year follow-up, 29 children were re-assessed. After clinical examination, the caries increment was calculated (ΔDMFT) and correlated with the baseline clinical variables and the QLF readings. Results showed a significant positive correlation between ΔQ1 min and the ΔDMFT (r = 0.44, p = 0.02). The ΔDMFT was significantly correlated with the baseline deft (r = 0.56, p = 0.002), cavitated active caries lesions (r = 0.52, p = 0.003), and filled teeth (r = 0.53, p = 0.003). In a regression analysis the use of fluoridated salt (SC = –0.10) and fluoride gel (SC = –0.14) were negatively associated with ΔDMFT. In conclusion, these findings suggest that the demineralisation properties of the etched sites and the outcome of the 24-hour measurements with QLF are significantly associated with caries increment. Previous caries experience strongly correlated with caries increment in this group of children

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

Retinal Temperature Determination Based on Photopic Porcine Electroretinogram

Objective: Subthreshold retinal laser therapy (SLT) is a treatment modality where the temperature of the retinal pigment epithelium (RPE) is briefly elevated to trigger the therapeutic benefits of sublethal heat shock. However, the temperature elevation induced by a laser exposure varies between patients due to individual differences in RPE pigmentation and choroidal perfusion. This study describes an electroretinography (ERG)-based method for controlling the temperature elevation during SLT. Methods: The temperature dependence of the photopic ERG response kinetics were investigated both ex vivo with isolated pig retinas and in vivo with anesthetized pigs by altering the temperature of the subject and recording ERG in different temperatures. A model was created for ERG-based temperature estimation and the feasibility of the model for controlling SLT was assessed through computational simulations. Results: The kinetics of the photopic in vivo flash ERG signaling accelerated between 3.6 and 4.7%/degrees C, depending on the strength of the stimulus. The temperature dependence was 5.0%/degrees C in the entire investigated range of 33 to 44 degrees C in ex vivo ERG. The simulations showed that the method is suitable for determining the steady-state temperature elevation in SLT treatments with a sufficiently long laser exposure and large spot size, e.g., during > 30 s laser exposures with > 3 mm stimulus spot diameter. Conclusions: The described ERG-based temperature estimation model could be used to control SLT treatments such as transpupillary thermotherapy. Significance: The introduced ERG-based method for controlling SLT could improve the repeatability, safety, and efficacy of the treatment of various retinal disorders.Peer reviewe

Chaperone-assisted translocation of a polymer through a nanopore

Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy $\epsilon$ between the chaperone and the chain and the chaperone concentration $N_c$ can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time $\tau$ has a transition from long-tailed distribution to Gaussian distribution with increasing $\epsilon$. $\tau$ rapidly decreases and then almost saturates with increasing binding energy for short chain, however, it has a minimum for longer chains at lower chaperone concentration. We also show that $\tau$ has a minimum as a function of the chaperone concentration. For different $\epsilon$, a nonuniversal dependence of $\tau$ on the chain length $N$ is also observed. These results can be interpreted by characteristic entropic effects for flexible polymers induced by either crowding effect from high chaperone concentration or the intersegmental binding for the high binding energy.Comment: 10 pages, to appear in J. Am. Chem. So

Criteria and geological setting for the generic geothermal underground research laboratory, GEOLAB

High flow rate injection and related hydromechanical interaction are the most important factors in reservoir development of Enhanced Geothermal Systems (EGS). GeoLaB, a new generic geothermal underground research laboratory (URL), is proposed for controlled high flow rate experiments (CHFE) to address limited comprehension of coupled processes connected to EGS reservoir flow conditions. As analogue for typical EGS development, CHFE require specific hydromechanical conditions including a connected fracture network in crystalline basement rock, sufficient hydraulic fracture transmissivities, a strike-slip to normal faulting tectonic regime, controllable hydraulic boundary conditions, and hydrothermal alteration fracture fillings that improve conditions for hydromechanical interaction. With the aim to identify most appropriate areas for future site selection, four criteria have been established based on the EGS reference site of Soultz. Two URLs in crystalline basement worldwide approximate the requirements of a new generic GeoLaB and may be used for accompanying experimentation. Besides favourable geological, hydraulic, and stress conditions, the vicinity to long-term EGS production favours the southern Black Forest as potential region for GeoLaB. Therefore, an exemplary site assessment has been carried out at “Wilhelminenstollen” in the southern Black Forest (Germany). New remote sensing, hydrochemical, and geophysical analyses as well as reactivation potential, and stress modelling were added to complement existing geological and hydrogeological information. At this site, reactivation potential analysis reveals two local maxima prone for shear reactivation as strike-slip faults. The highest lineament density is observed for the N110°E strike direction that is associated with both slip and dilation tendency maxima. Clay minerals occur in fractures and the matrix. Local, partly water-bearing fractures, when partly filled with ore minerals, were connected to veins in the tunnel using shallow geophysical methods. Hydrochemical data reveal infiltration of the tunnel water from at least 500 m above the tunnel. The results suggest a crystalline basement with a fracture network that is regionally connected and water-conducting. Hydraulic conductivity in the southern Black Forest granite is estimated to amount to about 4.5·10−8 m s−1 at 500 m depth. The hydraulic boundary conditions exclude unknown drainage. Analyses of the influence of topography on orientation and magnitude of the maximum stress indicate a minimum overburden of about 500 m for regional reactivation to be valid. In conclusion, the southern Black Forest and in particular “Wilhelminenstollen” offers favourable condition for CHFE. Final decision on the GeoLaB site is to be drawn from forthcoming exploration wells

Rapid VAC high dose melphalan regimen, a novel chemotherapy approach in childhood soft tissue sarcomas.

Forty-three children with malignant soft tissue sarcomas (IRS Groups II-IV) were treated with rapid dose delivery chemotherapy protocol comprising six courses of vincristine, adriamycin and cyclophosphamide, given in most cases within 8 weeks (Rapid VAC). This was followed in 36 patients by high dose melphalan with autologous bone marrow rescue. Twenty-six patients also received irradiation to the site of primary tumour. The Rapid VAC regimen was well tolerated and largely administered as an out-patient. There was one toxic death which occurred 2 months after high dose melphalan due to a combination of infection and possible anthracycline cardiomyopathy. Stages were, (Intergroup Rhabdomyosarcoma Study (IRS) system) Group, Group II--four patients. Group III--27 patients and Group IV--12 patients; International Society of Paediatric Oncology (SIOP) staging, Stage I--11, Stage II--13, Stage III--7, Stage IV--12. Actuarial survival at 5 years for all stages is 57% and event free survival 44%. For patients with non-metastatic diseases, 62% and 53% respectively. This treatment strategy utilises the philosophy of rapid drug delivery with high dose consolidation and enables all chemotherapy to be finished within a 4 month period. In general, a conservative approach was applied to both radiation and surgery to minimise late sequelae related to these treatment modalities. Although the small number of high risk patients in this study limits conclusions regarding efficacy in these subgroups the overall results with this regimen appear to be comparable to that with other approaches

Dragging a polymer chain into a nanotube and subsequent release

We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves the tube. MC simulations were performed for a self-avoiding lattice model with a biased chain growth algorithm, the pruned-enriched Rosenbluth method. The nanotube is a long channel opened at one end and its diameter $D$ is much smaller than the size of the polymer coil in solution. We analyze the following characteristics as functions of the chain end position $x$ inside the tube: the free energy of confinement, the average end-to-end distance, the average number of imprisoned monomers, and the average stretching of the confined part of the chain for various values of $D$ and for the number of monomers in the chain, $N$. We show that when the chain end is dragged by a certain critical distance $x^*$ into the tube, the polymer undergoes a first-order phase transition whereby the remaining free tail is abruptly sucked into the tube. This is accompanied by jumps in the average size, the number of imprisoned segments, and in the average stretching parameter. The critical distance scales as $x^*\sim ND^{1-1/\nu}$. The transition takes place when approximately 3/4 of the chain units are dragged into the tube. The theory presented is based on constructing the Landau free energy as a function of an order parameter that provides a complete description of equilibrium and metastable states. We argue that if the trapped chain is released with all monomers allowed to fluctuate, the reverse process in which the chain leaves the confinement occurs smoothly without any jumps. Finally, we apply the theory to estimate the lifetime of confined DNA in metastable states in nanotubes.Comment: 13pages, 14figure

Directed motion emerging from two coupled random processes: Translocation of a chain through a membrane nanopore driven by binding proteins

We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and partially prevent backsliding of the polymer through the pore. The process is characterized by the rates: k for the polymer to make a diffusive jump through the pore, q for unbinding of a chaperone, and the rate q kappa for binding (with a binding strength kappa); except for the case of no binding kappa=0 the presence of the chaperones give rise to an effective force that drives the translocation process. Based on a (2+1) variate master equation, we study in detail the coupled dynamics of diffusive translocation and (partial) rectification by the binding proteins. In particular, we calculate the mean translocation time as a function of the various physical parameters.Comment: 22 pages, 5 figures, IOP styl