http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Synthetic molecular motors and mechanical machines.

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Over the 100 years since its discovery, liquid crystals have been the intriguing subject for both academia and industries. The textbook of de Gennes The Physics of Liquid Crystals published in 1974 is still the bible for many LC researchers, but new subjects unmentioned in the book have also risen for these years. This chapter describes the story of the recent developments and the future perspectives in physics of liquid crystals, especially focusing on the contributions by Japanese research groups for the last decade.

Physics of Liquid Crystals

Dynamic atomic force microscopy methods

Kabatana takedai (Microspora) is known as an enzootic pathogen of salmonids in limited water systems such as the Chitose River in Hokkaido, northern Japan. In this study, susceptibility to K. takedai was compared among masu salmon Oncorhynchus masou originating from the Chitose River, Shiribetsu River and Shari River, and rainbow trout O. mykiss from Shizuoka Prefecture, Japan. After exposure of fish to the Chitose River water, cysts of K. takedai in the heart and trunk muscle were examined by microscopy. Prevalence and intensity of infection were not considerably different among the three populations of masu salmon, whereas rainbow trout was more susceptible to K. takedai than masu salmon, particularly in the heart. A newly developed PCR test showed the higher percentage of fish with pre-cyst stage of K. takedai in the heart of rainbow trout than in masu salmon, suggesting that K. takedai established the cardiac infection at early stages more in rainbow trout than in masu salmon. A histopathological observation indicated that K. takedai infection in the heart caused granulomatous inflammation characterized by fibrinoid degeneration, but there was no difference in the progress of the inflammation between the two fish species.

Comparison of Susceptibility to Kabatana takedai (Microspora) among Salmonid Fishes

Several new benzoic acid derivatives having perfluorinated substituents were synthesized and their hydrogen-bonded complexes with 4, 4’-dipyridyl were prepared. In these acid/base complexes the incompatibility between perfluoroalkyl moieties and hydrocarbon parts is large, which can lead to organize nano-segregation structures. We have found in one of such complexes, that has a long flexible fluorinated moiety, a thermotropic cubic phase with Ia3d symmetry formed by double gyroid of two interpenetrating jointed rod networks with an estimated cell parameter of 10.9 nm. Furthermore another complex with a branched long perfluoroalkyl terminal chain exhibits a first order smectic A to smectic C phase transition, which is confirmed with thermal analysis detecting a large enthalpy change of 5.3 kJxmol-1, X-ray scattering experiments revealing a tilt angle jump, and polarized optical microscopy observing a remarkable texture change at the phase transition temperature.

Liquid Crystalline Nano-Segregated Structures in Hydrogen-Bonded Complexes of Fluoroalkyl Substituted Benzoic Acids

/pdf/flexural-behavior-of-rc-beams-strengthened-with-frp-bars-by-1szipf6iff.pdf

Flexural Behavior of RC Beams Strengthened with FRP Bars by Near-Surface Mounted Method

Biaxial nematic liquid crystals have attracted much attention from both fundamental and application points of view,
because the fast response based on the rotation of the minor director is expected. So far, different molecular designs have
been proposed for the emergence of the biaxial nematic phase. Among that, we have been interested in applying "preorganization"
concept on generating the biaxiality. Dimeric liquid crystal compounds have been prepared in line with
this concept in which two mesogenic parts are linked by the biphenyl connecting group. The pre-organized dimmer
shows an anomalous textural change, for vertically-aligned and free-standing film samples, at the smectic C (SmC)-
nematic (N) phase transition, in which the Schlieren texture of the SmC changes into the other Schlieren texture of the N
phase. There are two possible explanations for this textural change, i.e., the occurrence of the director change at the
SmC-N phase transition or the emergence of biaxiality in the N phase. The electric-field-induced birefringence has also
been measured in detail for investigating the biaxial nature of the sample.

Pre-organized liquid crystals:biaxial nature of laterally-connected dimer

Electroclinic measurements, in which an applied electric field E induces a rotation Δθ ([proportional]E) of the liquid crystal director about the electric field axis in a chiral environment, were performed on several configurationally achiral liquid crystals in the presence of an imposed helical director profile. This imposed twist establishes a chiral symmetry environment for the liquid crystal. It was observed that a conformationally racemic mesogen possessing a flexible phenyl benzoate core exhibits a measurable electroclinic response in the nematic phase. On the other hand, when the phenyl benzoate mesogen is mixed with a mesogen containing a rigid, conformationally achiral core (fluorenone), or with a racemic dopant with an axially chiral core that mimics a mesogen having rigid right- and left-handed conformations (2,2'-spirobiindan-1,1'-dione), the magnitudes of the electroclinic responses were found to decrease sharply, apparently going to zero when extrapolated to the pure 2,2'-spirobiindan-1,1'-dione or fluorenone limit. (Note that neither of these additives possesses a nematic phase.). The results suggest that the flexibility of the core and its ability to deracemize conformationally in order to compensate the elastic energy cost of the imposed twist is the primary mechanism behind the observed electroclinic response.

/pdf/nematic-molecular-core-flexibility-and-chiral-induction-4d4w5w07zr.pdf

Hiroshi Yokoyama

Papers

Comparison of Susceptibility to Kabatana takedai (Microspora) among Salmonid Fishes

Liquid Crystalline Nano-Segregated Structures in Hydrogen-Bonded Complexes of Fluoroalkyl Substituted Benzoic Acids

Flexural Behavior of RC Beams Strengthened with FRP Bars by Near-Surface Mounted Method

Pre-organized liquid crystals:biaxial nature of laterally-connected dimer

Nematic molecular core flexibility and chiral induction.