Decoding Single Molecule Time Traces with Dynamic Disorder

Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm - Variational Bayes-double chain Markov model (VB-DCMM) - to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na$^+$ solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA

On the origin of the hump structure in the in-plane optical conductivity of high Tc cuprates based on a SU(2) slave-boson theory

An improved version of SU(2) slave-boson approach is applied to study the in-plane optical conductivity of the two dimensional systems of high Tc cuprates. We investigate the role of fluctuations of both the phase and amplitude of order parameters on the (Drude) peak-dip-hump structure in the in-plane conductivity as a function of hole doping concentration and temperature. The mid-infrared(MIR) hump in the in-plane optical conductivity is shown to originate from the antiferromagnetic spin fluctuations of short range(the amplitude fluctuations of spin singlet pairing order parameters), which is consistent with our previous U(1) study. However the inclusion of both the phase and amplitude fluctuations is shown to substantially improve the qualitative feature of the optical conductivity by showing substantially reduced Drude peak widths for entire doping range. Both the shift of the hump position to lower frequency and the growth of the hump peak height with increasing hole concentration is shown to be consistent with observations.Comment: 7 pages, 6 figure

High-efficiency Bidirectional Buck-Boost Converter for Residential Energy Storage System

This paper proposes a bidirectional dc-dc converter for residential micro-grid applications. The proposed converter can operate over an input voltage range that overlaps the output voltage range. This converter uses two snubber capacitors to reduce the switch turn-off losses, a dc-blocking capacitor to reduce the input/output filter size, and a 1:1 transformer to reduce core loss. The windings of the transformer are connected in parallel and in reverse-coupled configuration to suppress magnetic flux swing in the core. Zero-voltage turn-on of the switch is achieved by operating the converter in discontinuous conduction mode. The experimental converter was designed to operate at a switching frequency of 40-210 kHz, an input voltage of 48 V, an output voltage of 36-60 V, and an output power of 50-500 W. The power conversion efficiency for boost conversion to 60 V was >= 98.3% in the entire power range. The efficiency for buck conversion to 36 V was >= 98.4% in the entire power range. The output voltage ripple at full load was <3.59 V-p.p for boost conversion (60 V) and 1.35 V-p.p for buck conversion (36 V) with the reduced input/output filter. The experimental results indicate that the proposed converter is well-suited to smart-grid energy storage systems that require high efficiency, small size, and overlapping input and output voltage ranges.11Ysciescopu

Insight into highly conserved H1 subtype-specific epitopes in influenza virus hemagglutinin

Influenza viruses continuously undergo antigenic changes with gradual accumulation of mutations in hemagglutinin (HA) that is a major determinant in subtype specificity. The identification of conserved epitopes within specific HA subtypes gives an important clue for developing new vaccines and diagnostics. We produced and characterized nine monoclonal antibodies that showed significant neutralizing activities against H1 subtype influenza viruses, and determined the complex structure of HA derived from a 2009 pandemic virus A/Korea/01/2009 (KR01) and the Fab fragment from H1-specific monoclonal antibody GC0587. The overall structure of the complex was essentially identical to the previously determined KR01 HA-Fab0757 complex structure. Both Fab0587 and Fab0757 recognize readily accessible head regions of HA, revealing broadly shared and conserved antigenic determinants among H1 subtypes. The beta-strands constituted by Ser110-Glu115 and Lys169-Lys170 form H1 epitopes with distinct conformations from those of H1 and H3 HA sites. In particular, Glu112, Glu115, Lys169, and Lys171 that are highly conserved among H1 subtype HAs have close contacts with HCDR3 and LCDR3. The differences between Fab0587 and Fab0757 complexes reside mainly in HCDR3 and LCDR3, providing distinct antigenic determinants specific for 1918 pdm influenza strain. Our results demonstrate a potential key neutralizing epitope important for H1 subtype specificity in influenza virus