A two-state model for helicase translocation and unwinding of nucleic acids

Helicases are molecular motors that unwind double-stranded nucleic acids (dsNA), such as DNA and RNA). Typically a helicase translocates along one of the NA single strands while unwinding and uses adenosine triphosphate (ATP) hydrolysis as an energy source. Here we model of a helicase motor that can switch between two states, which could represent two different points in the ATP hydrolysis cycle. Our model is an extension of the earlier Betterton-J\"ulicher model of helicases to incorporate switching between two states. The main predictions of the model are the speed of unwinding of the dsNA and fluctuations around the average unwinding velocity. Motivated by a recent claim that the NS3 helicase of Hepatitis C virus follows a flashing ratchet mechanism, we have compared the experimental results for the NS3 helicase with a special limit of our model which corresponds to the flashing ratchet scenario. Our model accounts for one key feature of the experimental data on NS3 helicase. However, contradictory observations in experiments carried out under different conditions limit the ability to compare the model to experiments.Comment: minor modification

The temperature dependence of the isothermal bulk modulus at 1 bar pressure

It is well established that the product of the volume coefficient of thermal expansion and the bulk modulus is nearly constant at temperatures higher than the Debye temperature. Using this approximation allows predicting the values of the bulk modulus. The derived analytical solution for the temperature dependence of the isothermal bulk modulus has been applied to ten substances. The good correlations to the experiments indicate that the expression may be useful for substances for which bulk modulus data are lacking

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

Stochastic Description of a Bistable Frustrated Unit

Mixed positive and negative feedback loops are often found in biological systems which support oscillations. In this work we consider a prototype of such systems, which has been recently found at the core of many genetic circuits showing oscillatory behaviour. Our model consists of two interacting species A and B, where A activates not only its own production, but also that of its repressor B. While the self-activation of A leads already to a bistable unit, the coupling with a negative feedback loop via B makes the unit frustrated. In the deterministic limit of infinitely many molecules, such a bistable frustrated unit is known to show excitable and oscillatory dynamics, depending on the maximum production rate of A which acts as a control parameter. We study this model in its fully stochastic version and we find oscillations even for parameters which in the deterministic limit are deeply in the fixed-point regime. The deeper we go into this regime, the more irregular these oscillations are, becoming finally random excitations whenever fluctuations allow the system to overcome the barrier for a large excursion in phase space. The fluctuations can no longer be fully treated as a perturbation. The smaller the system size (the number of molecules), the more frequent are these excitations. Therefore, stochasticity caused by demographic noise makes this unit even more flexible with respect to its oscillatory behaviour.Comment: 28 pages, 17 figure

Metal-Organic Frameworks in Germany: from Synthesis to Function

Metal-organic frameworks (MOFs) are constructed from a combination of inorganic and organic units to produce materials which display high porosity, among other unique and exciting properties. MOFs have shown promise in many wide-ranging applications, such as catalysis and gas separations. In this review, we highlight MOF research conducted by Germany-based research groups. Specifically, we feature approaches for the synthesis of new MOFs, high-throughput MOF production, advanced characterization methods and examples of advanced functions and properties

Estimation of the advection effects induced by surface heterogeneities in the surface energy budget

Peer ReviewedPostprint (published version

Diagnosing the Clumpy Protoplanetary Disk of the UXor Type Young Star GM Cephei

UX Orionis stars (UXors) are Herbig Ae/Be or T Tauri stars exhibiting sporadic occultation of stellar light by circumstellar dust. GM\,Cephei is such a UXor in the young ($\sim4$~Myr) open cluster Trumpler\,37, showing prominent infrared excess, emission-line spectra, and flare activity. Our photometric monitoring (2008--2018) detects (1)~an $\sim$3.43~day period, likely arising from rotational modulation by surface starspots, (2)~sporadic brightening on time scales of days due to accretion, (3)~irregular minor flux drops due to circumstellar dust extinction, and (4)~major flux drops, each lasting for a couple of months with a recurrence time, though not exactly periodic, of about two years. The star experiences normal reddening by large grains, i.e., redder when dimmer, but exhibits an unusual "blueing" phenomenon in that the star turns blue near brightness minima. The maximum extinction during relatively short (lasting $\leq 50$~days) events, is proportional to the duration, a consequence of varying clump sizes. For longer events, the extinction is independent of duration, suggestive of a transverse string distribution of clumps. Polarization monitoring indicates an optical polarization varying $\sim3\%$--8$\%$, with the level anticorrelated with the slow brightness change. Temporal variation of the unpolarized and polarized light sets constraints on the size and orbital distance of the circumstellar clumps in the interplay with the young star and scattering envelope. These transiting clumps are edge-on manifestations of the ring- or spiral-like structures found recently in young stars with imaging in infrared of scattered light, or in submillimeter of thermalized dust emission.Comment: 20 pages, 9 figure

Clustering analysis of noise sources in healthcare facilities

Hospital environmental noise can impact the comfort of both workers and patients, causing sleep disturbances and hindering the recovery process. Environmental noise in hospitals is typically due to the mixture of various sound sources, including staff, outdoor noises, and mechanical equipment. Patients and staff experience different effects from noise contributions: the former's recovery process is influenced, while the latter's communication efficiency is compromised. Conventional measurements are based on equivalent continuous sound pressure levels. However, the latter does not provide any kind of details about the hospital's sound context. Unsupervised acoustic measurements have been already used in many fields, but still in a few healthcare scenarios. For this reason, a clustering technique has been used to deepen the conventional noise analysis. The Gaussian Mixture Model (GMM) is used to identify and quantify the contributions of the main types of sound sources. This analysis has been conducted within two four-bed bays: one in active conditions and the other unoccupied. The GMM analysis involves the noisiest period of the day, the morning round. The results demonstrate the GMM's ability to overcome conventional practices by providing significant insight into environmental noise, even in active conditions. In the active room, noise sources were tagged and measured. The spectral matching, based on the empty room's outcomes and standard references, represents the benchmark to assess the reliability of the method