Stable Frank-Kasper phases of self-assembled, soft matter spheres

Single molecular species can self-assemble into Frank Kasper (FK) phases, finite approximants of dodecagonal quasicrystals, defying intuitive notions that thermodynamic ground states are maximally symmetric. FK phases are speculated to emerge as the minimal-distortional packings of space-filling spherical domains, but a precise quantitation of this distortion and how it affects assembly thermodynamics remains ambiguous. We use two complementary approaches to demonstrate that the principles driving FK lattice formation in diblock copolymers emerge directly from the strong-stretching theory of spherical domains, in which minimal inter-block area competes with minimal stretching of space-filling chains. The relative stability of FK lattices is studied first using a diblock foam model with unconstrained particle volumes and shapes, which correctly predicts not only the equilibrium {\sigma} lattice, but also the unequal volumes of the equilibrium domains. We then provide a molecular interpretation for these results via self-consistent field theory, illuminating how molecular stiffness regulates the coupling between intra-domain chain configurations and the asymmetry of local packing. These findings shed new light on the role of volume exchange on the formation of distinct FK phases in copolymers, and suggest a paradigm for formation of FK phases in soft matter systems in which unequal domain volumes are selected by the thermodynamic competition between distinct measures of shape asymmetry.Comment: 40 pages, 22 figure

DNA in Nanochannels - Theory and Applications

Nanofluidic structures have over the last two decades emerged as a powerful platform for detailed analysis of DNA on the kilobase pair length scale. When DNA is confined to a nanochannel, the combination of excluded volume and DNA stiffness leads to the DNA being stretched to near its full contour length. Importantly, this stretching takes place at equilibrium, without any chemical modifications to the DNA. As a result, any DNA can be analyzed, such as DNA extracted from cells or circular DNA, and it is relatively easy to study reactions on the ends of linear DNA. In this comprehensive review, we first give a thorough description of the current understanding of the polymer physics of DNA and how that leads to stretching in nanochannels. We then describe how the versatility of nanofabrication can be used to design devices specifically tailored for the problem at hand, either by controlling the degree of confinement or enabling facile exchange of reagents to measure DNA-protein reaction kinetics. The remainder of the review focuses on two important applications of confining DNA in nanochannels. The first is optical DNA mapping, which provides kilobase pair resolution of the genomic sequence of intact DNA molecules in excess of 100 kilobase pairs in size through labeling strategies that are suitable for fluorescence microscopy. In this section, we highlight solutions to the technical aspects of genomic mapping, rather than recent applications in human genetics, including the use of enzyme-based labeling and affinity-based labeling to produce the genomic maps. The second is DNA-protein interactions, and several recent examples of such studies on DNA compaction, filamentous protein complexes, and reactions with the chain ends are presented. Taken together, these two applications demonstrate the power of DNA confinement and nanofluidics in genomics, molecular biology and biophysics

Convective dispersion without molecular diffusion

A method-of-moments scheme is invoked to compute the asymptotic, long-time mean (or composite) velocity and dispersivity (effective diffusivity) of a two-state particle undergoing one-dimensional convective-diffusive motion accompanied by a reversible linear transition (``chemical reaction'' or ``change in phase'') between these states. The instantaneous state-specific particle velocity is assumed to depend only upon the instantaneous state of the particle, and the transition between states is assumed to be governed by spatially-independent, first-order kinetics. Remarkably, even in the absence of molecular diffusion, the average transport of the ``composite'' particle exhibits gaussian diffusive behavior in the long-time limit, owing to the effectively stochastic nature of the overall transport phenomena induced by the interstate transition. The asymptotic results obtained are compared with numerical computations.Comment: to appear in Physica

Alpha-Synuclein Modulates the Physical Properties of DNA

Published by Wiley-VCH Verlag GmbH & Co. KGaA. Fundamental research on Parkinson\u27s disease (PD) most often focuses on the ability of α-synuclein (aS) to form oligomers and amyloids, and how such species promote brain cell death. However, there are indications that aS also plays a gene-regulatory role in the cell nucleus. Here, the interaction between monomeric aS and DNA in vitro has been investigated with single-molecule techniques. Using a nanofluidic channel system, it was discovered that aS binds to DNA and by studying the DNA–protein complexes at different confinements we determined that aS binding increases the persistence length of DNA from 70 to 90 nm at high coverage. By atomic force microscopy it was revealed that at low protein-to-DNA ratio, the aS binding occurs as small protein clusters scattered along the DNA; at high protein-to-DNA ratio, the DNA is fully covered by protein. As DNA-aS interactions may play roles in PD, it is of importance to characterize biophysical properties of such complexes in detail

Breast cancer detection: radiologists’ performance using mammography with and without automated whole-breast ultrasound

ObjectiveRadiologist reader performance for breast cancer detection using mammography plus automated whole-breast ultrasound (AWBU) was compared with mammography alone.MethodsScreenings for non-palpable breast malignancies in women with radiographically dense breasts with contemporaneous mammograms and AWBU were reviewed by 12 radiologists blinded to the diagnoses; half the studies were abnormal. Readers first reviewed the 102 mammograms. The American College of Radiology (ACR) Breast Imaging Reporting and Data System (BIRADS) and Digital Mammographic Imaging Screening Trial (DMIST) likelihood ratings were recorded with location information for identified abnormalities. Readers then reviewed the mammograms and AWBU with knowledge of previous mammogram-only evaluation. We compared reader performance across screening techniques using absolute callback, areas under the curve (AUC), and figure of merit (FOM).ResultsTrue positivity of cancer detection increased 63%, with only a 4% decrease in true negativity. Reader-averaged AUC was higher for mammography plus AWBU compared with mammography alone by BIRADS (0.808 versus 0.701) and likelihood scores (0.810 versus 0.703). Similarly, FOM was higher for mammography plus AWBU compared with mammography alone by BIRADS (0.786 versus 0.613) and likelihood scores (0.791 versus 0.614).ConclusionAdding AWBU to mammography improved callback rates, accuracy of breast cancer detection, and confidence in callbacks for dense-breasted women

The Breadth, but Not the Magnitude, of Circulating Memory B Cell Responses to P. falciparum Increases with Age/Exposure in an Area of Low Transmission

BACKGROUND: Malaria caused by Plasmodium falciparum remains a major cause of death in sub-Saharan Africa. Immunity against symptoms of malaria requires repeated exposure, suggesting either that the parasite is poorly immunogenic or that the development of effective immune responses to malaria may be impaired. METHODS: We carried out two age-stratified cross-sectional surveys of anti-malarial humoral immune responses in a Gambian village where P. falciparum malaria transmission is low and sporadic. Circulating antibodies and memory B cells (MBC) to four malarial antigens were measured using ELISA and cultured B cell ELISpot. FINDINGS AND CONCLUSIONS: The proportion of individuals with malaria-specific MBC and antibodies, and the average number of antigens recognised by each individual, increased with age but the magnitude of these responses did not. Malaria-specific antibody levels did not correlate with either the prevalence or median number of MBC, indicating that these two assays are measuring different aspects of the humoral immune response. Among those with immunological evidence of malaria exposure (defined as a positive response to at least one malarial antigen either by ELISA or ELISPOT), the median number of malaria-specific MBC was similar to median numbers of diphtheria-specific MBC, suggesting that the circulating memory cell pool for malaria antigens is of similar size to that for other antigens