Toy amphiphiles on the computer: What can we learn from generic models?

Generic coarse-grained models are designed such that they are (i) simple and (ii) computationally efficient. They do not aim at representing particular materials, but classes of materials, hence they can offer insight into universal properties of these classes. Here we review generic models for amphiphilic molecules and discuss applications in studies of self-assembling nanostructures and the local structure of bilayer membranes, i.e. their phases and their interactions with nanosized inclusions. Special attention is given to the comparison of simulations with elastic continuum models, which are, in some sense, generic models on a higher coarse-graining level. In many cases, it is possible to bridge quantitatively between generic particle models and continuum models, hence multiscale modeling works on principle. On the other side, generic simulations can help to interpret experiments by providing information that is not accessible otherwise.Comment: Invited feature article, to appear in Macromolecular Rapid Communication

Hard X-ray Fourier transform holography from an array of oriented referenced objects

The use of multiple, oriented and singly referenced objects was evaluated as a means to overcome the low scattering cross section inherent in hard X-ray Fourier transform holography. It is shown that the image of each object can be restored as in the conventional single-object case

New structure around 3250 MeV in the baryonic B decay and the D0∗(2400)ND^*_0(2400)N molecular hadron

In this work, we first propose the isovector $nD^{*}_0(2400)^0$ molecular state to explain the enhancement structure around 3250 MeV ($X_c(3250)^0$) in the $\Sigma_c^{++}\pi^-\pi^-$ invariant mass spectrum newly observed by the BaBar Collaboration. Under this molecular state configuration, both the analysis of the mass spectrum and the study of its dominant decay channel can well depict its resonance parameters measured by BaBar. Our investigation also shows that the isovector $nD^{*}_0(2400)^0$ molecular state can decay into $\Sigma_c^{++}\pi^-\pi^-$, which is consistent with the experimental observation. These studies provide the direct support to the isovector $nD^{*}_0(2400)^0$ molecular state assignment to $X_c(3250)^0$.Comment: 5 pages, 1 table, 4 figures. Accepted by Eur. Phys. J.

The magnitude and timing of recalled immunity after breakthrough infection is shaped by SARS-CoV-2 variants

Vaccination against SARS-CoV-2 protects from infection and improves clinical outcomes in breakthrough infections, likely reflecting residual vaccine-elicited immunity and recall of immunological memory. Here, we define the early kinetics of spike-specific humoral and cellular immunity after vaccination of seropositive individuals and after Delta or Omicron breakthrough infection in vaccinated individuals. Early longitudinal sampling revealed the timing and magnitude of recall, with the phenotypic activation of B cells preceding an increase in neutralizing antibody titers. While vaccination of seropositive individuals resulted in robust recall of humoral and T cell immunity, recall of vaccine-elicited responses was delayed and variable in magnitude during breakthrough infections and depended on the infecting variant of concern. While the delayed kinetics of immune recall provides a potential mechanism for the lack of early control of viral replication, the recall of antibodies coincided with viral clearance and likely underpins the protective effects of vaccination against severe COVID-19

The open-charm radiative and pionic decays of molecular charmonium Y(4274)

In this work, we investigate the decay widths and the line shapes of the open-charm radiative and pionic decays of Y(4274) with the $D_s\bar{D}_{s0}(2317)$ molecular charmonium assignment. Our calculation indicates that the decay widths of $Y(4274)\to D^{+}_{s}D^{*-}_{s}\gamma$ and $Y(4274)\to D^+_{s}D^-_{s}\pi^0$ can reach up to 0.05 keV and 0.75 keV, respectively. In addition, the result of the line shape of the photon spectrum of $Y(4274)\to D_s^+ {D}_s^{*-} \gamma$ shows that there exists a very sharp peak near the large end point of photon energy. The line shape of the pion spectrum of $Y(4274)\to D_s^+ {D}_s^{*-} \pi^0$ is similar to that of the pion spectrum of $Y(4274)\to D_s^+ {D}_s^{*-} \gamma$, where we also find a very sharp peak near the large end point of pion energy. According to our calculation, we suggest further experiments to carry out the search for the open-charm radiative and pionic decays of Y(4274).Comment: 7 pages, 6 figures, 1 table. Published versio

Sequential Events in the Irreversible Thermal Denaturation of Human Brain-Type Creatine Kinase by Spectroscopic Methods

The non-cooperative or sequential events which occur during protein thermal denaturation are closely correlated with protein folding, stability, and physiological functions. In this research, the sequential events of human brain-type creatine kinase (hBBCK) thermal denaturation were studied by differential scanning calorimetry (DSC), CD, and intrinsic fluorescence spectroscopy. DSC experiments revealed that the thermal denaturation of hBBCK was calorimetrically irreversible. The existence of several endothermic peaks suggested that the denaturation involved stepwise conformational changes, which were further verified by the discrepancy in the transition curves obtained from various spectroscopic probes. During heating, the disruption of the active site structure occurred prior to the secondary and tertiary structural changes. The thermal unfolding and aggregation of hBBCK was found to occur through sequential events. This is quite different from that of muscle-type CK (MMCK). The results herein suggest that BBCK and MMCK undergo quite dissimilar thermal unfolding pathways, although they are highly conserved in the primary and tertiary structures. A minor difference in structure might endow the isoenzymes dissimilar local stabilities in structure, which further contribute to isoenzyme-specific thermal stabilities

Monotonicity of Fitness Landscapes and Mutation Rate Control

A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Much biological theory in this area is based on Ronald Fisher's work, who used Euclidean geometry to study the relation between mutation size and expected fitness of the offspring in infinite phenotypic spaces. Here we reconsider this theory based on the alternative geometry of discrete and finite spaces of DNA sequences. First, we consider the geometric case of fitness being isomorphic to distance from an optimum, and show how problems of optimal mutation rate control can be solved exactly or approximately depending on additional constraints of the problem. Then we consider the general case of fitness communicating only partial information about the distance. We define weak monotonicity of fitness landscapes and prove that this property holds in all landscapes that are continuous and open at the optimum. This theoretical result motivates our hypothesis that optimal mutation rate functions in such landscapes will increase when fitness decreases in some neighbourhood of an optimum, resembling the control functions derived in the geometric case. We test this hypothesis experimentally by analysing approximately optimal mutation rate control functions in 115 complete landscapes of binding scores between DNA sequences and transcription factors. Our findings support the hypothesis and find that the increase of mutation rate is more rapid in landscapes that are less monotonic (more rugged). We discuss the relevance of these findings to living organisms

Plant responses to photoperiod

Photoperiod controls many developmental responses in animals, plants and even fungi. The response to photoperiod has evolved because daylength is a reliable indicator of the time of year, enabling developmental events to be scheduled to coincide with particular environmental conditions. Much progress has been made towards understanding the molecular mechanisms involved in the response to photoperiod in plants. These mechanisms include the detection of the light signal in the leaves, the entrainment of circadian rhythms, and the production of a mobile signal which is transmitted throughout the plant. Flowering, tuberization and bud set are just a few of the many different responses in plants that are under photoperiodic control. Comparison of what is known of the molecular mechanisms controlling these responses shows that, whilst common components exist, significant differences in the regulatory mechanisms have evolved between these responses