On the lattice ground state of densely packed hard ellipses

Among lattice configurations of densely packed hard ellipses, Monte Carlo simulations are used to identify the so-called parallel and diagonal lattices as the two favorable states. The free energies of these two states are computed for several system sizes employing the Einstein crystal method. An accurate calculation of the free energy difference between the two states reveals the parallel lattice as the state with the lowest free energy. The origin of the entropic difference between the two states is further elucidated by assessing the roles of the translational and rotational degrees of freedom.

Kagome lattice made by impenetrable ellipses with attractive walls

Low-dimensional structures, such as the kagome lattice, are experiencing renewed interest within the physics, chemistry and materials science communities in terms of both basic and applied research. Herein, we show that stable kagome lattices can be made by hard-core ellipses with attractive walls. We study a model in which hard-core ellipse is covered uniformly by an attractive square-well layer. Analytical calculations predict that for certain combinations of the asphericity aspect ratio and the attraction range, the kagome lattice is the ground-state conformation of this model. For one specific set of parameters computer simulations prove that the kagome lattice is the lowest free energy structure at low temperatures. At high temperatures, the conformational ensemble is dominated by liquid states. The temperature at which transition from the liquid to the kagome structure occurs has a maximum as a function of density, indicating that the underlying phase transformation is re-entrant. The maximum is attributed to the energy difference between the liquid and crystalline states. Our study reveals that the kagome lattice can be produced by means of very simple models. No specifically designed molecular shapes or interactions are required. Instead, very basic physical characteristics, such as asphericity and uniform attraction, are sufficient to induce spontaneous transition into this structure. In the context of the general understanding of the self-assembly processes, this finding is encouraging, giving one hope that the requirements for the assembly of other low-dimensional structures could be equally simple.

Drug Screen Identifies Leflunomide for Treatment of Inflammatory Bowel Disease Caused by TTC7A Deficiency

BACKGROUND & AIMS

Mutations in the tetratricopeptide repeat domain 7A gene (TTC7A) cause intestinal epithelial and immune defects. Patients can become immune deficient and develop apoptotic enterocolitis, multiple intestinal atresia, and recurrent intestinal stenosis. The intestinal disease in patients with TTC7A deficiency is severe and untreatable, and it recurs despite resection or allogeneic hematopoietic stem cell transplant. We screened drugs for those that prevent apoptosis of in cells with TTC7A deficiency and tested their effects in an animal model of the disease.

METHODS

We developed a high-throughput screen to identify compounds approved by the US Food and Drug Administration that reduce activity of caspases 3 and 7 in TTC7A-knockout (TTC7A-KO) HAP1 (human haploid) cells and reduce the susceptibility to apoptosis. We validated the effects of identified agents in HeLa cells that stably express TTC7A with point mutations found in patients. Signaling pathways in cells were analyzed by immunoblots. We tested the effects of identified agents in zebrafish with disruption of ttc7a, which develop intestinal defects, and colonoids derived from biopsy samples of patients with and without mutations in TTC7A. We performed real-time imaging of intestinal peristalsis in zebrafish and histologic analyses of intestinal tissues from patients and zebrafish. Colonoids were analyzed by immunofluorescence and for ion transport.

RESULTS

TTC7A-KO HAP1 cells have abnormal morphology and undergo apoptosis, due to increased levels of active caspases 3 and 7. We identified drugs that increased cell viability; leflunomide (used to treat patients with inflammatory conditions) reduced caspase 3 and 7 activity in cells by 96%. TTC7A-KO cells contained cleaved caspase 3 and had reduced levels of phosphorylated AKT and X-linked inhibitor of apoptosis (XIAP); incubation of these cells with leflunomide increased levels of phosphorylated AKT and XIAP and reduced levels of cleaved caspase 3. Administration of leflunomide to ttc7a^-/- zebrafish increased gut motility, reduced intestinal tract narrowing, increased intestinal cell survival, increased sizes of intestinal luminal spaces, and restored villi and goblet cell morphology. Exposure of patient-derived colonoids to leflunomide increased cell survival, polarity, and transport function.

CONCLUSIONS

In a drug screen, we identified leflunomide as an agent that reduces apoptosis and activates AKT signaling in TTC7A-KO cells. In zebrafish with disruption of ttc7a, leflunomide restores gut motility, reduces intestinal tract narrowing, and increases intestinal cell survival. This drug might be repurposed for treatment of TTC7A deficiency.

Softness and non-spherical shape define the phase behavior and the structural properties of lysozyme in aqueous solutions

In this study, Boltzmann inversion is applied in conjunction with molecular dynamics simulations to derive inter-molecular potential for protein lysozyme in aqueous solution directly from experimental static structure factor. The potential has a soft repulsion at short distances and an attraction well at intermediate distances that give rise to the liquid-liquid phase separation. Moreover, Gibbs ensemble Monte Carlo simulations demonstrate that a non-spherical description of lysozyme is better suited to correctly reproduce the experimentally observed properties of such a phase separation. Our findings shed new light on the common problem in molecular and cell biology: "How to model proteins in their natural aqueous environments?"

Effects of hydrodynamic retardation and interparticle interactions on the self-assembly in a drying droplet containing suspended solid particles

Self-assembly of particles, suspended in a drying droplet, were studied by the Monte Carlo method. The Brownian diffusion of particles was simulated accounting for the effect of hydrodynamic retardation and interparticle interactions. The model allowed for explaining formation of the "coffee ring" patterns even without accounting for the radial flows towards the three-phase contact line. Morphologies of the drying patterns and their dependence on interparticle interactions and concentration of particles are discussed.

Resorufin Butyrate as a Soluble and Monomeric High-Throughput Substrate for a Triglyceride Lipase

Triglyceride lipases such as lipoprotein lipase, endothelial lipase, and hepatic lipase play key roles in controlling the levels of plasma lipoprotein. Accordingly, small-molecule modulation of these species could alter patient lipid profiles with corresponding health effects. Screening of these enzymes for small-molecule therapeutics has historically involved the use of lipid-based particles to mimic native substrates. However, particle-based artifacts can complicate the discovery of therapeutic molecules. As a simplifying solution, the authors sought to develop an approach involving a soluble and monomeric lipase substrate. Using purified bovine lipoprotein lipase as a model system, they show that the hydrolysis of resorufin butyrate can be fluorescently monitored to give a robust assay (Z′ > 0.8). Critically, using parallel approaches, they show that resorufin butyrate is soluble and monomeric under assay conditions. The presented assay should be useful as a simple and inexpensive primary or secondary screen for the discovery of therapeutic lipase modulators.

EXP6 fluids at extreme conditions modeled by two-Yukawa potentials

A two-Yukawa representation of the EXP6 fluids at supercritical temperatures and high pressures has been developed and examined using molecular simulations. A uniquely defined mapping of the repulsive part of the EXP6 potential curve onto the two-Yukawa potential is used. Two ranges of temperatures, one encountered in geochemical applications (T(geo) range) and the other at conditions of detonations (T(det) range), are considered and it is shown that the local structures of both fluids are practically identical. Deviations between the EXP6 and two-Yukawa potential functions at intermediate separations lead to differences in the thermodynamic properties of the two fluids at lower temperatures of the T(geo) range; at higher temperatures and in the high T(det) temperature range both the structural and thermodynamic properties of the EXP6 and two-Yukawa fluids are practically identical.

Novel perturbation approach for the structure factor of the attractive hard-core Yukawa fluid

A novel perturbation approach for the structure factor S(k) of the Lennard-Jones-type Yukawa fluid with z=1.8 is presented. An approach is based on a new reference system, that is, the short-range Yukawa model with z0>z=1.8. By choosing for the reference system the value z0=6, it is shown that (i) the proposed approach for S(k) performs much better than the traditional hard-sphere reference perturbation method does; (ii) the use of an approximate mean spherical (MSA) description of the reference structure factor provides the results for S(k) that are more accurate as those obtained from the direct MSA computations; and (iii) the results obtained for S(k) tend to reproduce "exact" simulation results when accurate simulation data for the reference system are used.

Modeling and measurement of the detector presampling MTF of a variable resolution x-ray CT scanner

The detector presampling modulation transfer function (MTF) of a 576-channel variable resolution x-ray (VRX) computed tomography (CT) scanner was evaluated in this study. The scanner employs a VRX detector, which provides increased spatial resolution by matching the scanner's field of view (FOV) to the size of an object being imaged. Because spatial resolution is the parameter the scanner promises to improve, the evaluation of this resolution is important. The scanner's pre-reconstruction spatial resolution, represented by the detector presampling MTF, was evaluated using both modeling (Monte Carlo simulation) and measurement (the moving slit method). The theoretical results show the increase in the cutoff frequency of the detector presampling MTF from 1.39 to 43.38 cycles/mm as the FOV of the VRX CT scanner decreases from 32 to 1 cm. The experimental results are in reasonable agreement with the theoretical data. Some discrepancies between the measured and the modeled detector presampling MTFs can be explained by the limitations of the model. At small FOVs (1-8 cm), the MTF measurements were limited by the size of the focal spot. The obtained results are important for further development of the VRX CT scanner.

Determination of calibration parameters of a VRX CT system using an "Amoeba" algorithm

Efforts to improve the spatial resolution of CT scanners have focused mainly on reducing the source and detector element sizes, ignoring losses from the size of the secondary-ionization charge "clouds" created by the detected x-ray photons, i.e., the "physics limit." This paper focuses on implementing a technique called "projective compression." which allows further reduction in effective cell size while overcoming the physics limit as well. Projective compression signifies detector geometries in which the apparent cell size is smaller than the physical cell size, allowing large resolution boosts. A realization of this technique has been developed with a dual-arm "variable-resolution x-ray" (VRX) detector. Accurate values of the geometrical parameters are needed to convert VRX outputs to formats ready for optimal image reconstruction by standard CT techniques. The required calibrating data are obtained by scanning a rotating pin and fitting a theoretical parametric curve (using a multi-parameter minimization algorithm) to the resulting pin sinogram. Excellent fits are obtained for both detector-arm sections with an average (maximum) fit deviation of ~0.05 (0.1) detector cell width. Fit convergence and sensitivity to starting conditions are considered. Pre- and post-optimization reconstructions of the alignment pin and a biological subject reconstruction after calibration are shown.

Attitude changes following a sexual counseling program for spinal cord injured persons

The attitudes of a sample of spinal cord injured outpatients toward a range of sexual behaviors were measured before and after participation in a counseling program. In comparison to the sexual attitudes of an untreated control group those of the sample group were found to be more permissive after than before the program. In addition, the counseling program, which operated in a workshop format over a period of 6 weeks, was favorably evaluated by participants on a number of criteria.