Modelling DNA Origami Self-Assembly at the Domain Level

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami

An Examination of the Feasibility of Linear Deterministic Sea Wave Prediction in Multi-Directional Seas Using Wave Profiling Radar: Theory, Simulation and Sea Trials

This is the final version of the article. Available from the American Meteorological Society via the DOI in this record.For a number of maritime tasks there is a short time period, typically only a few tens of seconds, where a critical event occurs which defines a limiting wave height for the whole operation. Examples are the recovery of fixed and rotary winged aircraft, cargo transfers, final pipe mating in fluid transfer operations and launch/recovery of small craft. The recovery of a 30 ton rescue submersible onto a mother ship in the NATO Submarine Rescue System is a prime example. In such applications short term Deterministic Sea Wave Prediction (DSWP) can play a vital role in extending the sea states under which the system can be safely deployed. DSWP also has great potential in conducting experimental sea wave research at full scale. This report explores the feasibility of using data from an experimental wave profiling radar in achieving DSWP. The report includes theory, simulation and field testing. Two forms of DSWP are employed, a fixed point system based upon a restricted set of wave directions, from which we obtain some success, and the other a fully two dimensional technique, which requires further development. The main finding is that using wave profiling radar for DSWP offers promise but requires improvements both to the spatial reliability and resolution of the wave profiling radar, and to the temporal resolution of its sweep before the technique can be considered to be viable as a usable tool.The authors acknowledge funding from the European Union FP7 and U.K. Ministry of Defence NSRS projects

A Laboratory Investigation of Supersonic Clumpy Flows: Experimental Design and Theoretical Analysis

We present a design for high energy density laboratory experiments studying the interaction of hypersonic shocks with a large number of inhomogeneities. These ``clumpy'' flows are relevant to a wide variety of astrophysical environments including the evolution of molecular clouds, outflows from young stars, Planetary Nebulae and Active Galactic Nuclei. The experiment consists of a strong shock (driven by a pulsed power machine or a high intensity laser) impinging on a region of randomly placed plastic rods. We discuss the goals of the specific design and how they are met by specific choices of target components. An adaptive mesh refinement hydrodynamic code is used to analyze the design and establish a predictive baseline for the experiments. The simulations confirm the effectiveness of the design in terms of articulating the differences between shocks propagating through smooth and clumpy environments. In particular, we find significant differences between the shock propagation speeds in a clumpy medium compared to a smooth one with the same average density. The simulation results are of general interest for foams in both inertial confinement fusion and laboratory astrophysics studies. Our results highlight the danger of using average properties of inhomogeneous astrophysical environments when comparing timescales for critical processes such as shock crossing and gravitational collapse times.Comment: 7 pages, 6 figures. Submitted to the Astrophysical Journal. For additional information, including simulation animations and the pdf and ps files of the paper with embedded high-quality images, see http://pas.rochester.edu/~wm

Perforated Sheets as the Porous Material for a Suction-flap Application

Two-dimensional tests were made of an NACA 0006 airfoil with area suction applied to a porous region on a 0.3-chord trailing-edge flap deflected 50 degrees. The lift with suction approached the value computed from thin-airfoil theory. The lift gains and suction quantity requirements were unaffected by the perforation patterns of the surface over a wide range of hole sizes and spacings

Collective molecule formation in a degenerate Fermi gas via a Feshbach resonance

We model collisionless collective conversion of a degenerate Fermi gas into bosonic molecules via a Feshbach resonance, treating the bosonic molecules as a classical field and seeding the pairing amplitudes with random phases. A dynamical instability of the Fermi sea against association into molecules initiates the conversion. The model qualitatively reproduces several experimental observations {[Regal et al., Nature {\bf 424}, 47 (2003)]}. We predict that the initial temperature of the Fermi gas sets the limit for the efficiency of atom-molecule conversion.Comment: 4 pages, 3 figures, 10+ references, accepted to PR

Cutaneous leiomyosarcoma arising in a smallpox scar

BACKGROUND: Cutaneous leiomyosarcoma (CLM) is a very rare smooth muscle tumour that accounts for about 2–3% of all superficial soft tissue sarcomas. Although the development of various malignancies in scar tissue is well known, we report the first case of a CLM developing in a small pox scar. CASE PRESENTATION: A 66-year-old man presented with a painless, slow-growing lump in a small pox scar on his left shoulder. Histological biopsies showed the lesion to be a primary, well-differentiated cutaneous leiomyosarcoma. A CT scan of the thorax was conducted, which showed no signs of metastases. The complete lesion was then surgically excised, and histopathological examination revealed a radically excised cutaneous type leiomyosarcoma After 13 months’ review the patient was doing well with no evidence of tumour recurrence. CONCLUSIONS: This is the first report of a CLM arising in a small pox scar. Although the extended time interval between scarring and malignant changes makes it difficult to advise strict follow-up for patients with small pox scars, one should be aware that atypical changes and/or symptoms occurring in a small pox scar could potentially mean malignant transformation

Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation

Background DNA methylation and histone deacetylation are epigenetic mechanisms that play major roles in eukaryotic gene regulation. We hypothesize that many genes in the human hepatoma cell line HepG2 are regulated by DNA methylation and histone deacetylation. Treatment with 5-aza-2'-deoxycytidine (5-aza-dC) to inhibit DNA methylation with and/or Trichostatin A (TSA) to inhibit histone deacetylation should allow us to identify genes that are regulated epigenetically in hepatoma cells. Results 5-aza-dC had a much larger effect on gene expression in HepG2 cells than did TSA, as measured using Affymetrix® HG-U133 Plus 2.0 microarrays. The expression of 1504 probe sets was affected by 5-aza-dC (at p < 0.01), 535 probe sets by TSA, and 1929 probe sets by the combination of 5-aza-dC and TSA. 5-aza-dC treatment turned on the expression of 211 probe sets that were not detectably expressed in its absence. Expression of imprinted genes regulated by DNA methylation, such as H19 and NNAT, was turned on or greatly increased in response to 5-aza-dC. Genes involved in liver processes such as xenobiotic metabolism (CYP3A4, CYP3A5, and CYP3A7) and steroid biosynthesis (CYP17A1 and CYP19A1), and genes encoding CCAAT element-binding proteins (C/EBPα, C/EBPβ, and C/EBPγ) were affected by 5-aza-dC or the combination. Many of the genes that fall within these groups are also expressed in the developing fetal liver and adult liver. Quantitative real-time RT-PCR assays confirmed selected gene expression changes seen in microarray analyses. Conclusion Epigenetics play a role in regulating the expression of several genes involved in essential liver processes such as xenobiotic metabolism and steroid biosynthesis in HepG2 cells. Many genes whose expression is normally silenced in these hepatoma cells were re-expressed by 5-aza-dC treatment. DNA methylation may be a factor in restricting the expression of fetal genes during liver development and in shutting down expression in hepatoma cells