Biomolecular System Design: Architecture, Synthesis, and Simulation

The advancements in systems and synthetic biology have been broadening the range of realizable systems with increasing complexity both in vitro and in vivo. Systems for digital logic operations, signal processing, analog computation, program flow control, as well as those composed of different functions – for example an on-site diagnostic system based on multiple biomarker measurements and signal processing – have been realized successfully. However, the efforts to date tend to tackle each design problem separately, relying on ad hoc strategies rather than providing more general solutions based on a unified and extensible architecture, resulting in long development cycle and rigid systems that require redesign even for small specification changes.Inspired by well-tested techniques adopted in electronics design automation (EDA), this work aims to remedy current design methodology by establishing a standardized, complete flow for realizing biomolecular systems. Given a behavior specification, the flow streamlines all the steps from modeling, synthesis, simulation, to final technology mapping onto implementing chassis. The resulted biomolecular systems of our design flow are all built on top of an FPGA-like reconfigurable architecture with recurring modules. Each module is designed the function of eachmodule depends on the concentrations of assigned auxiliary species acting as the “tuning knobs.” Reconfigurability not only simplifies redesign for altered specification or post-simulation correction, but also makes post-manufacture fine-tuning – even after system deployment – possible. This flexibility is especially important in synthetic biology due to the unavoidable variations in both the deployed biological environment and the biomolecular reactions forming the designed system.In fact, by combining the system’s reconfigurability and neural network’s self-adaptiveness through learning, we further demonstrate the high compatibility of neuromorphic computation to our proposed architecture. Simulation results verified that with each module implementing a neuron of selected model (ex. spike-based, threshold-gate-like, etc.), accompanied by an appropriate choice of reconfigurable properties (ex. threshold value, synaptic weight, etc.), the system built from our proposed flow can indeed perform desired neuromorphic functions

Vermonters’ Opinions on Low-Dose CT Lung Cancer Screening

Introduction: Lung cancer is the number one cause of cancer death among men and women in Vermont and the United States. Smoking increases the risk of lung cancer—nearly 90% of lung cancer is due to smoking. Frequently, lung cancers do not present clinically until they are advanced stage and therefore prognosis is poor. However, if detected early lung cancers are more operable and patients have better outcomes. In December 2013 the US Preventive Services Task Force released new guidelines for lung cancer screening among current and former smokers ages 55 to 80. It is recommended that current and former (within 15 years of quitting) smokers of 30 pack years receive an annual low-dose CT scan. The objective of this project was to assess the level of knowledge and attitudes towards lung cancer screening with low-dose CT scanning among Vermonters in the Burlington area.https://scholarworks.uvm.edu/comphp_gallery/1205/thumbnail.jp

The Light Curve of the Weakly-Accreting T Tauri Binary KH 15D from 2005-10: Insights into the Nature of its Protoplanetary Disk

Photometry of the unique pre-main sequence binary system KH 15D is presented, spanning the years 2005-2010. This system has exhibited photometric variations and eclipses over the last 50 years caused by a precessing circumbinary disk. Advancement of the occulting edge across the binary orbit has continued and the photospheres of both stars are now completely obscured at all times. The system is now visible only by scattered light, and yet it continues to show a periodic variation on the orbital cycle with an amplitude exceeding two magnitudes. This variation, which depends only on the binary phase, has likely been present in the data since at least 1995. It can, by itself, account for shoulders on the light curve prior to ingress and following egress, obviating the need for components of extant models such as a scattering halo around star A or forward scattering from a fuzzy disk edge. A plausible source for the variable scattering component is reflected light from the far side of a warped occulting disk. We have detected color changes in V-I of several tenths of a magnitude to both the blue and red that occur during times of minima. These may indicate the presence of a third source of light (faint star) within the system, or a change in the reflectance properties of the disk as the portion being illuminated varies with the orbital motion of the stars. The data support a picture of the circumbinary disk as a geometrically thin, optically thick layer of perhaps mm or cm-sized particles that has been sculpted by the binary stars and possibly other components into a decidedly nonplanar configuration. A simple (infinitely sharp) knife-edge model does a good job of accounting for all of the recent (2005-2010) occultation data.Comment: To appear in The Astronomical Journa

Abrupt change in tropical Pacific climate mean state during the Little Ice Age

The mean state of the tropical Pacific ocean-atmosphere climate, in particular its east-west asymmetry, has profound consequences for regional climates and for the El Niño/Southern Oscillation variability. Here we present a new high-resolution paleohydrological record using the stable-hydrogen-isotopic composition of terrestrial-lipid biomarkers (δDwax) from a 1,400-year-old lake sedimentary sequence from northern Philippines. Results show a dramatic and abrupt increase in δDwax values around 1630 AD with sustained high values until around 1900 AD. We interpret this change as a shift to significantly drier conditions in the western tropical Pacific during the second half of the Little Ice Age as a result of a change in tropical Pacific mean state tied to zonal sea surface temperature (SST) gradients. Our findings highlight the prominent role of abrupt shifts in zonal SST gradients on multidecadal to multicentennial timescales in shaping the tropical Pacific hydrology of the last millennium, and demonstrate that a marked transition in the tropical Pacific mean state can occur within a period of a few decades.publishedVersio

Growth mechanism of dendritic hematite via hydrolysis of ferricyanide

W.Z. thanks EPSRC for financial support to purchase the FEG SEM (EP/F019580/1).The detailed process of the hydrolysis of ferricyanide into dendritic α-Fe2O3 (hematite) crystals with snowflake-like, feather-like and leaf-like morphologies has been investigated. [Fe(CN)6]3– anions were found to polymerize into large, disordered soft matter aggregates at an early stage. The nucleation of hematite crystals took place near the surface of these aggregates via further hydrolysis. After the crystals grew to a certain size, branches started to appear. When the concentration of ferricyanide was low (i.e. 2 mM to 3.8 mM), growth was preferentially along the six equivalent directions, resulting in a flat snowflake-like shape, while high concentrations (i.e. 9 mM to 500 mM) of ferricyanide led to the growth of selective directions along the zone axes, forming a feather-like or leaf-like morphology. Highly selective adsorption and surface hydrolysis of [Fe(CN)6]3– anions on α-Fe2O3 crystals was found to be a crucial process in the formation of these novel morphologies. It was found that the polymeri- sation of ferricyanide led to a reduction of pH value and that the formation of Fe2O3 increased pH value. The pH value of the solution at the point when the branches start to grow can significantly affect the distribution of Lewis acidic sites on different surfaces and, therefore, change the growth direction. The newly established mechanism is complementary to the classical theories of crystal growth.PostprintPeer reviewe

Printed electronics

Printed electronic device comprising a substrate onto at least one surface of which has been applied a layer of an electrically conductive ink comprising functionalized graphene sheets and at least one binder. A method of preparing printed electronic devices is further disclosed

Printed Electronics

Printed electronic device comprising a substrate onto at least one surface of which has been applied a layer of an electrically conductive ink comprising functionalized graphene sheets and at least one binder. A method of preparing printed electronic devices is further disclosed