Reversing a granular flow on a vibratory conveyor

Experimental results are presented on the transport properties of granular materials on a vibratory conveyor. For circular oscillations of the shaking trough a non-monotonous dependence of the transport velocity on the normalized acceleration is observed. Two maxima are separated by a regime, where the granular flow is much slower and, in a certain driving range, even reverses its direction. A similar behavior is found for a single solid body with a low coefficient of restitution, whereas an individual glass bead of 1 mm diameter is propagated in the same direction for all accelerations.Comment: 4 pages, 5 figures, submitted to Applied Physics Letter

Porcelain-Fused-to-Titanium Restorations From Implant Level - Preliminary Observations

Until a few years ago use of the abutment was necessary for making fixed restorations retained on Branemark implants. For multiple-unit restorations, abutments served as a”misfit eliminating zone” for the framework cast with gold alloy. Single crowns were made as restorations cemented on prefabricated abutments. Thanks to the use of modern laboratory methods, it is now possible to produce multiple-unit restorations retained directly on implants with the metal part made of titanium alloy. One such method is the All-in-One system, in which the metal part of the restoration is made of one piece of titanium, with the use of a computer aided milling machine. Thanks to the development in porcelain fusing to titanium, it is also possible to make single crowns as a screw-retained restoration seated directly on an implant. For this purpose, TiAdapt abutments were used with own modification of UCLA-type crown production. The paper describes some advantages and disadvantages of the above mentioned systems and basics of their use. The study group consisted of 22 restorations (12 bridges and 10 crowns) made for 14 patients. Most of them (18) were made for the lower jaw. All bridges were twoor three-unit restorations. The observation period was from three months up to two years. Complications were observed in two cases. Both of them consisted of cracks in the porcelain. Due to the design of the restorations, the complications were eliminated without any problems. A possible cause of the porcelain cracking was the excessive bulk of the porcelain in areas where there had been lack of metal support for the veneering layer. Due to the easy application and positive aesthetic and functional results the described methods seem to be worth recommending, with some clinical limitations

The morphology and application of stem cells in digestive system surgery

Background: Stem cells constitute a group of cells which possess the ability to self-renew as well as the capacity to differentiate into a vast number of different cells within the human organism. Moreover, stem cells are able to undergo a potentially unlimited number of divisions and this characteristic is clinically essential. Specific fields of its application include treatment of diseases mainly in the field of haematology, orthopaedics, surgery, dentistry, and neurology. Materials and methods: In the following work, the current knowledge concerning mechanisms of stem cell treatment in different parts of the digestive system with its diseases as well as adjacent therapy for surgery has been revised. Results: Stem cells therapy may be used in the treatment of various diseases of different parts of the digestive system. This also applies to the end part of the digestive tract (proctological diseases) because stem cells can be used to treat fistulas. Liposuction allows more recovery of mesenchymal stem cells, compared to previous bone marrow harvesting methods. Despite the application of stem cells in the treatment of different diseases used for many years so far, the therapeutic use for the regeneration of the gastrointestinal tract is still rare and unfamiliar. Conclusions: Regenerative medicine seems to be a promising tool in medical research, especially when insulated cells and designed biomaterials are taken into consideration. Major points of discussion include types of stem cells, their origin or differentiation for the treatment of many diseases

Modeling the pharmacodynamics of passive membrane permeability

Small molecule permeability through cellular membranes is critical to a better understanding of pharmacodynamics and the drug discovery endeavor. Such permeability may be estimated as a function of the free energy change of barrier crossing by invoking the barrier domain model, which posits that permeation is limited by passage through a single “barrier domain” and assumes diffusivity differences among compounds of similar structure are negligible. Inspired by the work of Rezai and co-workers (JACS 128:14073–14080, 2006), we estimate this free energy change as the difference in implicit solvation free energies in chloroform and water, but extend their model to include solute conformational affects. Using a set of eleven structurally diverse FDA approved compounds and a set of thirteen congeneric molecules, we show that the solvation free energies are dominated by the global minima, which allows solute conformational distributions to be effectively neglected. For the set of tested compounds, the best correlation with experiment is obtained when the implicit chloroform global minimum is used to evaluate the solvation free energy difference

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Biallelic variants in ADAMTS15 cause a novel form of distal arthrogryposis

Purpose We aimed to identify the underlying genetic cause for a novel form of distal arthrogryposis. Methods Rare variant family-based genomics, exome sequencing, and disease-specific panel sequencing were used to detect ADAMTS15 variants in affected individuals. Adamts15 expression was analyzed at the single-cell level during murine embryogenesis. Expression patterns were characterized using in situ hybridization and RNAscope. Results We identified homozygous rare variant alleles of ADAMTS15 in 5 affected individuals from 4 unrelated consanguineous families presenting with congenital flexion contractures of the interphalangeal joints and hypoplastic or absent palmar creases. Radiographic investigations showed physiological interphalangeal joint morphology. Additional features included knee, Achilles tendon, and toe contractures, spinal stiffness, scoliosis, and orthodontic abnormalities. Analysis of mouse whole-embryo single-cell sequencing data revealed a tightly regulated Adamts15 expression in the limb mesenchyme between embryonic stages E11.5 and E15.0. A perimuscular and peritendinous expression was evident in in situ hybridization in the developing mouse limb. In accordance, RNAscope analysis detected a significant coexpression with Osr1, but not with markers for skeletal muscle or joint formation. Conclusion In aggregate, our findings provide evidence that rare biallelic recessive trait variants in ADAMTS15 cause a novel autosomal recessive connective tissue disorder, resulting in a distal arthrogryposis syndrome

Enumerating Pathways of Proton Abstraction Based on a Spatial and Electrostatic Analysis of Residues in the Catalytic Site

The pathways of proton abstraction (PA), a key aspect of most catalytic reactions, is often controversial and highly debated. Ultrahigh-resolution diffraction studies, molecular dynamics, quantum mechanics and molecular mechanic simulations are often adopted to gain insights in the PA mechanisms in enzymes. These methods require expertise and effort to setup and can be computationally intensive. We present a push button methodology – Proton abstraction Simulation (PRISM) – to enumerate the possible pathways of PA in a protein with known 3D structure based on the spatial and electrostatic properties of residues in the proximity of a given nucleophilic residue. Proton movements are evaluated in the vicinity of this nucleophilic residue based on distances, potential differences, spatial channels and characteristics of the individual residues (polarity, acidic, basic, etc). Modulating these parameters eliminates their empirical nature and also might reveal pathways that originate from conformational changes. We have validated our method using serine proteases and concurred with the dichotomy in PA in Class A β-lactamases, both of which are hydrolases. The PA mechanism in a transferase has also been corroborated. The source code is made available at www.sanchak.com/prism

Mutation of Archaeal Isopentenyl Phosphate Kinase Highlights Mechanism and Guides Phosphorylation of Additional Isoprenoid Monophosphates

I sopentenyl diphosphate (IPP) and its isomeric part-ner dimethylallyl diphosphate (DMAPP) are precur-sors for a diverse collection of primary and second-ary isoprenoid metabolites in all organisms. Following its formation, successive units of IPP are used together either with DMAPP, formed by the action of types I or II IPP isomerases, or with the IPP extended isoprenoid diphosphate chain, to biosynthesize C10, C15, or C20 oligoprenyl diphosphates known as geranyl diphos-phate (GPP), farnesyl diphosphate (FPP), and gera-nylgeranyl diphosphate (GGPP), respectively, as well as larger isoprenoid diphosphates. In plants and some mi-croorganisms, GPP, FPP, and GGPP also serve as start-ingmaterials for the biosynthesis of a large class of spe-cialized and often cyclic terpene hydrocarbons (1). FPP is the most ubiquitous of the three isoprenoid diphos-phate building blocks, as it resides at the juncture of bi

A modified Ehrenfest formalism for efficient large-scale ab initio molecular dynamics

We present in detail the recently derived ab-initio molecular dynamics (AIMD) formalism [Phys. Rev. Lett. 101 096403 (2008)], which due to its numerical properties, is ideal for simulating the dynamics of systems containing thousands of atoms. A major drawback of traditional AIMD methods is the necessity to enforce the orthogonalization of the wave-functions, which can become the bottleneck for very large systems. Alternatively, one can handle the electron-ion dynamics within the Ehrenfest scheme where no explicit orthogonalization is necessary, however the time step is too small for practical applications. Here we preserve the desirable properties of Ehrenfest in a new scheme that allows for a considerable increase of the time step while keeping the system close to the Born-Oppenheimer surface. We show that the automatically enforced orthogonalization is of fundamental importance for large systems because not only it improves the scaling of the approach with the system size but it also allows for an additional very efficient parallelization level. In this work we provide the formal details of the new method, describe its implementation and present some applications to some test systems. Comparisons with the widely used Car-Parrinello molecular dynamics method are made, showing that the new approach is advantageous above a certain number of atoms in the system. The method is not tied to a particular wave-function representation, making it suitable for inclusion in any AIMD software package.Comment: 28 pages, 5 figures, published in a special issue of J. Chem. Theory Comp. in honour of John Perde