AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation

The thermodynamic driving force in the self-assembly of the secondary structure of a class of donor-acceptor oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy AFM experiments. The oligorotaxanes consist of cyclobis(paraquat-\emph{p}-phenylene) rings threaded onto an oligomer of 1,5-dioxynaphthalenes linked by polyethers. The simulations are performed in a high dielectric medium using MM3 as the force field. The resulting force vs. extension isotherms show a mechanically unstable region in which the molecule unfolds and, for selected extensions, blinks in the force measurements between a high-force and a low-force regime. From the force vs. extension data the molecular potential of mean force is reconstructed using the weighted histogram analysis method and decomposed into energetic and entropic contributions. The simulations indicate that the folding of the oligorotaxanes is energetically favored but entropically penalized, with the energetic contributions overcoming the entropy penalty and effectively driving the self-assembly. In addition, an analogy between the single-molecule folding/unfolding events driven by the AFM tip and the thermodynamic theory of first-order phase transitions is discussed and general conditions, on the molecule and the cantilever, for the emergence of mechanical instabilities and blinks in the force measurements in equilibrium isometric pulling experiments are presented. In particular, it is shown that the mechanical stability properties observed during the extension are intimately related to the fluctuations in the force measurements.Comment: 42 pages, 17 figures, accepted to the Journal of Chemical Physic

A microfluidic chip based model for the study of full thickness human intestinal tissue using dual flow

© 2016 Author(s). The study of inflammatory bowel disease, including Ulcerative Colitis and Crohn's Disease, has relied largely upon the use of animal or cell culture models; neither of which can represent all aspects of the human pathophysiology. Presented herein is a dual flow microfluidic device which holds full thickness human intestinal tissue in a known orientation. The luminal and serosal sides are independently perfused ex vivo with nutrients with simultaneous waste removal for up to 72 h. The microfluidic device maintains the viability and integrity of the tissue as demonstrated through Haematoxylin & Eosin staining, immunohistochemistry and release of lactate dehydrogenase. In addition, the inflammatory state remains in the tissue after perfusion on the device as determined by measuring calprotectin levels. It is anticipated that this human model will be extremely useful for studying the biology and tes ting novel interventions in diseased tissue

Steric constraints in model proteins

A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable. Furthermore, several of the encodable structures are highly designable and are the non-degenerate ground state of several sequences. Even though the native state conformations are typically compact, not all compact conformations are encodable. The incorporation of the hydrophobic and polar nature of amino acids further enhances the attractive features of the model.Comment: RevTex, 5 pages, 3 postscript figure

Career planning courses increase career readiness of graduate and postdoctoral trainees

BACKGROUND: Given national calls for intentional career development during graduate and post-graduate scientific training, this study assessed career readiness development within the context of academic career courses. The current study evaluated the effects of academic career courses offered at two institutions that were specifically designed to increase career awareness, interest, and career-related confidence among doctoral students and postdoctoral fellows. METHODS: Participants enrolled in a career course at trainees' respective academic institutions and responded to pre- and post-course surveys (n=32, n=148). The paper offers a thematic analysis of each of the two courses using an individualized learning plan career development framework and describes the results of their respective pretest-posttest evaluations which indicated increases in career readiness. RESULTS: Though the format and content provided in each course varied, participation was associated with increases in career readiness. Participants reported increased career-awareness including a greater familiarity with different types of careers overall. Furthermore, interest in tenure track faculty careers increased in both samples, which may assuage fears that exposure to diverse career pathways could reduce interest in academic careers. Transferrable skills, including career planning and awareness also significantly increased. Course participants reported an increase in the number and type of mentors they interacted with beyond their principal faculty mentor (other faculty, professional PhDs, peers, and administrative staff). CONCLUSIONS: Findings provide supporting evidence for the benefits of implementing structured career development efforts during PhD training; even with varying content, delivery methods, and instructor type, both academic career courses led to significant gains in career awareness and readiness. Successful development and delivery of academic career courses, with a focus on career planning skills, suggest that institutions can utilize these and are an effective way to prepare PhDs for their transition from training positions into careers.DP7 OD020317 - NIH HHS; P20 GM121327 - NIGMS NIH HHS; P30 CA177558 - NCI NIH HHS; R01 GM140282 - NIGMS NIH HHSPublished versio

Surface Enhanced Second Harmonic Generation from Macrocycle, Catenane, and Rotaxane Thin Films: Experiments and Theory

Surface enhanced second harmonic generation (SE SHG) experiments on molecular structures, macrocycles, catenanes, and rotaxanes, deposited as monolayers and multilayers by vacuum sublimation on silver, are reported. The measurements show that the molecules form ordered thin films, where the highest degree of order is observed in the case of macrocycle monolayers and the lowest in the case of rotaxane multilayers. The second harmonic generation activity is interpreted in terms of electric field induced second harmonic (EFISH) generation where the electric field is created by the substrate silver atoms. The measured second order nonlinear optical susceptibility for a rotaxane thin film is compared with that obtained by considering only EFISH contribution to SHG intensity. The electric field on the surface of a silver layer is calculated by using the Delphi4 program for structures obtained with TINKER molecular mechanics/dynamics simulations. An excellent agreement is observed between the calculated and the measured SHG susceptibilities.

52. Development of network of cancer family syndrome registries in eastern Europe

It has been proven that organizing the registries of families affected by CFS is very helpful in research leading to: 1. Identification of new genes of CFS, 2. Better knowledge of correlations in CFS, 3. Identification of external factors having impact on mutated genes, 4. Description of mutation characteristic for particular populations.Thus, development of CFS registries is very important for increasing pre-clinical and clinical research facilities. Direct positive consequence will also be the improvement of quality of life by better management of patients affected by CFS. Without registries these patients are very often not identified and deprived of appropriate recommendations concerning prophylactics, surveillance and treatment. Development of CFS registries leads also to further improvement of quality of life by progress in management in families with these tumours which can be achieved by better organizing of research on CFS. Better management in CFS families decreases also health-care costs by lowering the number of cancers and increasing the number of tumours detected at their earliest clinical stage when the treatment is less expensive.The scientific objectives of the project include:-elaboration of standards for a model cancer family syndrome registries in Eastern Europe-registration of ∼ 2000 families with different types of CFS in populations of East European countries (Czech, Hungary, Latvia, Lithuania, Poland)-initiation of European collaborative studies with the use of material collected by East European CFS registries

Supernova Remnants as Clues to Their Progenitors

Supernovae shape the interstellar medium, chemically enrich their host galaxies, and generate powerful interstellar shocks that drive future generations of star formation. The shock produced by a supernova event acts as a type of time machine, probing the mass loss history of the progenitor system back to ages of $\sim$ 10 000 years before the explosion, whereas supernova remnants probe a much earlier stage of stellar evolution, interacting with material expelled during the progenitor's much earlier evolution. In this chapter we will review how observations of supernova remnants allow us to infer fundamental properties of the progenitor system. We will provide detailed examples of how bulk characteristics of a remnant, such as its chemical composition and dynamics, allow us to infer properties of the progenitor evolution. In the latter half of this chapter, we will show how this exercise may be extended from individual objects to SNR as classes of objects, and how there are clear bifurcations in the dynamics and spectral characteristics of core collapse and thermonuclear supernova remnants. We will finish the chapter by touching on recent advances in the modeling of massive stars, and the implications for observable properties of supernovae and their remnants.Comment: A chapter in "Handbook of Supernovae" edited by Athem W. Alsabti and Paul Murdin (18 pages, 6 figures

An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints

In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the hard coordinates are fixed to configuration-dependent values). The presented scheme is exact, it does not contain any tunable parameter, and it only requires the calculation and inversion of a sub-block of the Hessian matrix of second derivatives of the function through which the constraints are defined. We also present a practical application to the case in which the sought observables are the Euclidean coordinates of complex molecular systems, and the function whose minimization defines the constraints is the potential energy. Finally, and in order to validate the method, which, as far as we are aware, is the first of its kind in the literature, we compare it to the natural and straightforward finite-differences approach in three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptideComment: 13 pages, 8 figures, published versio