Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains

We present a combined mean-field and simulation approach to different models describing the dynamics of classes formed by elements that can appear, disappear or copy themselves. These models, related to a paradigm duplication-innovation model known as Chinese Restaurant Process, are devised to reproduce the scaling behavior observed in the genome-wide repertoire of protein domains of all known species. In view of these data, we discuss the qualitative and quantitative differences of the alternative model formulations, focusing in particular on the roles of element loss and of the specificity of empirical domain classes.Comment: 10 Figures, 2 Table

Radiative lifetime measurements of rubidium Rydberg states

We have measured the radiative lifetimes of ns, np and nd Rydberg states of rubidium in the range 28 < n < 45. To enable long-lived states to be measured, our experiment uses slow-moving Rb atoms in a magneto-optical trap (MOT). Two experimental techniques have been adopted to reduce random and systematic errors. First, a narrow-bandwidth pulsed laser is used to excite the target Rydberg state, resulting in minimal shot-to-shot variation in the initial state population. Second, we monitor the target state population as a function of time delay from the laser pulse using a short-duration, millimetre-wave pulse that is resonant with a one- or two-photon transition. We then selectively field ionize the monitor state, and detect the resulting electrons with a micro-channel plate. This signal is an accurate mirror of the target state population, and is uncontaminated by contributions from other states which are populated by black body radiation. Our results are generally consistent with other recent experimental results obtained using a less sensitive method, and are also in excellent agreement with theory.Comment: 27 pages,6 figure

Measurement of the electric dipole moments for transitions to rubidium Rydberg states via Autler-Townes splitting

We present the direct measurements of electric-dipole moments for $5P_{3/2}\to nD_{5/2}$ transitions with $20<n<48$ for Rubidium atoms. The measurements were performed in an ultracold sample via observation of the Autler-Townes splitting in a three-level ladder scheme, commonly used for 2-photon excitation of Rydberg states. To the best of our knowledge, this is the first systematic measurement of the electric dipole moments for transitions from low excited states of rubidium to Rydberg states. Due to its simplicity and versatility, this method can be easily extended to other transitions and other atomic species with little constraints. Good agreement of the experimental results with theory proves the reliability of the measurement method.Comment: 12 pages, 6 figures; figure 6 replaced with correct versio

Robust Myco-Composites as a Platform for Versatile Hybrid-Living Structural Materials

Fungal mycelium, a living network of filamentous threads, thrives on lignocellulosic waste and exhibits rapid growth, hydrophobicity, and intrinsic regeneration, offering a potential means to create next-generation sustainable and functional composites. However, existing hybrid-living mycelium composites (myco-composites) are tremendously constrained by conventional mold-based manufacturing processes, which are only compatible with simple geometries and coarse biomass substrates that enable gas exchange. Here we introduce a class of structural myco-composites manufactured with a novel platform that harnesses high-resolution biocomposite additive manufacturing and robust mycelium colonization with indirect inoculation. We leverage principles of hierarchical composite design and selective nutritional provision to create a robust myco-composite that is scalable, tunable, and compatible with complex geometries. To illustrate the versatility of this platform, we characterize the impact of mycelium colonization on mechanical and surface properties of the composite, finding that it yields the strongest mycelium composite reported to date, and demonstrate fabrication of unique foldable bio-welded containers and flexible mycelium textiles. This study bridges the gap between biocomposite and hybrid-living materials research, opening the door to advanced structural mycelium applications and demonstrating a novel platform for development of diverse hybrid-living materials

Effect of photoions on the line shapes of the F\"orster resonance and microwave transitions in cold rubidium Rydberg atoms

Experiments on the spectroscopy of the F\"orster resonance Rb(37P)+Rb(37P) -> Rb(37S)+Rb(38S) and microwave transitions nP -> n'S, n'D between Rydberg states of cold Rb atoms in a magneto-optical trap have been performed. Under ordinary conditions, all spectra exhibited a 2-3 MHz line width independently of the interaction time of atoms with each other or with microwave radiation, although the ultimate resonance width should be defined by the inverse interaction time. Analysis of the experimental conditions has shown that the main source of the line broadening was the inhomogeneous electric field of cold photoions appeared at the excitation of initial Rydberg nP states by broadband pulsed laser radiation. Using an additional pulse of the electric field, which rapidly removed the photoions after the laser pulse, lead to a substantial narrowing of the microwave and F\"orster resonances. An analysis of various sources of the line broadening in cold Rydberg atoms has been conducted.Comment: 10 pages, 6 figure

Statistical Mechanics of Membrane Protein Conformation: A Homopolymer Model

The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results depending upon membrane permeability and polymer adsorptivity. For a membrane with the permeability larger than a critical value, the integration becomes the second order transition that occurs at the same temperature as that of the adsorption transition. For a nonadsorbing membrane, the integration is of the first order due to the aggregation of $\alpha$-helices.Comment: RevTeX with 5 postscript figure

Application of the Multi-modal Relevance Vector Machine to the Problem of Protein Secondary Structure Prediction

The aim of the paper is to experimentally examine the plausibility of Relevance Vector Machines (RVM) for protein secondary structure prediction. We restrict our attention to detecting strands which represent an especially problematic element of the secondary structure. The commonly adopted local principle of secondary structure prediction is applied, which implies comparison of a sliding window in the given polypeptide chain with a number of reference amino-acid sequences cut out of the training proteins as benchmarks representing the classes of secondary structure. As distinct from the classical RVM, the novel version applied in this paper allows for selective combination of several tentative window comparison modalities. Experiments on the RS126 data set have shown its ability to essentially decrease the number of reference fragments in the resulting decision rule and to select a subset of the most appropriate comparison modalities within the given set of the tentative ones. © 2012 Springer-Verlag

Energetic Components of Cooperative Protein Folding

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptide-like local conformational restrictions and environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure

Searching for New Physics beyond the Standard Model in Electric Dipole Moment

This is a theoretical review of exploration of new physics beyond the Standard Model (SM) in electric dipole moment (EDM) in elementary particles, atoms, and molecule. EDM is a very important CP violating phenomenon and sensitive to new physics. Starting with the estimations of EDM of quarks-leptons in the SM, we explore the new signals beyond the SM. However, these works drive us to more wide fronteers where we serach fundamental physics using atoms and molecules and vice versa. Paramagnetic atoms and molecules have great enhancement factor on electron EDM. Diamagnetic atoms and molecules are very sensitive to nuclear P and T odd processes. Thus the EDM becomes the key word not only of New Physics but also of unprecedented fruitful collaboration among particle, atomic. molecular physics. This review intends to help such collaboration over the wide range of physicists.Comment: 95pages. References are added. Appendix K is revise