Exploring the folding free energy surface of a three-helix bundle protein

The multidimensional free energy surface for a small fast folding helical protein is explored based on first-principle calculations. The model represents the 46-residue segment from fragment B of staphylococcal protein A. The relationship between collapse and tertiary structure formation, and the order of collapse and secondary structure formation, are investigated. We find that the initial collapse process gives rise to a transition state with about 30% of the native tertiary structure and 50–70% of the native helix content. We also observe two distinct distributions of native helix in this collapsed state (Rg ≈ 12 Å), one with about 20% of the native helical hydrogen bonds, the other with near 70%. The former corresponds to a local minimum. The barrier from this metastable state to the native state is about 2 kBT. In the latter case, folding is essentially a downhill process involving topological assembly. In addition, the order of formation of secondary structure among the three helices is examined. We observe cooperative formation of the secondary structure in helix I and helix II. Secondary structure in helix III starts to form following the formation of certain secondary structure in both helix I and helix II. Comparisons of our results with those from theory and experiment are made.

Field theory in superfluid 3He: What are the lessons for particle physics, gravity, and high-temperature superconductivity?

There are several classes of homogeneous Fermi systems that are characterized by the topology of the energy spectrum of fermionic quasiparticles: (i) gapless systems with a Fermi surface, (ii) systems with a gap in their spectrum, (iii) gapless systems with topologically stable point nodes (Fermi points), and (iv) gapless systems with topologically unstable lines of nodes (Fermi lines). Superfluid 3He-A and electroweak vacuum belong to the universality class 3. The fermionic quasiparticles (particles) in this class are chiral: they are left-handed or right-handed. The collective bosonic modes of systems of class 3 are the effective gauge and gravitational fields. The great advantage of superfluid 3He-A is that we can perform experiments by using this condensed matter and thereby simulate many phenomena in high energy physics, including axial anomaly, baryoproduction, and magnetogenesis. 3He-A textures induce a nontrivial effective metrics of the space, where the free quasiparticles move along geodesics. With 3He-A one can simulate event horizons, Hawking radiation, rotating vacuum, etc. High-temperature superconductors are believed to belong to class 4. They have gapless fermionic quasiparticles with a “relativistic” spectrum close to gap nodes, which allows application of ideas developed for superfluid 3He-A.

Effects of elevated atmospheric CO2 concentration on leaf dark respiration of Xanthium strumarium in light and in darkness

Leaf dark respiration (R) is an important component of plant carbon balance, but the effects of rising atmospheric CO2 on leaf R during illumination are largely unknown. We studied the effects of elevated CO2 on leaf R in light (RL) and in darkness (RD) in Xanthium strumarium at different developmental stages. Leaf RL was estimated by using the Kok method, whereas leaf RD was measured as the rate of CO2 efflux at zero light. Leaf RL and RD were significantly higher at elevated than at ambient CO2 throughout the growing period. Elevated CO2 increased the ratio of leaf RL to net photosynthesis at saturated light (Amax) when plants were young and also after flowering, but the ratio of leaf RD to Amax was unaffected by CO2 levels. Leaf RN was significantly higher at the beginning but significantly lower at the end of the growing period in elevated CO2-grown plants. The ratio of leaf RL to RD was used to estimate the effect of light on leaf R during the day. We found that light inhibited leaf R at both CO2 concentrations but to a lesser degree for elevated (17–24%) than for ambient (29–35%) CO2-grown plants, presumably because elevated CO2-grown plants had a higher demand for energy and carbon skeletons than ambient CO2-grown plants in light. Our results suggest that using the CO2 efflux rate, determined by shading leaves during the day, as a measure for leaf R is likely to underestimate carbon loss from elevated CO2-grown plants.

The Xanthophyll Cycle Modulates the Kinetics of Nonphotochemical Energy Dissipation in Isolated Light-Harvesting Complexes, Intact Chloroplasts, and Leaves of Spinach1

We analyzed the kinetics of nonphotochemical quenching of chlorophyll fluorescence (qN) in spinach (Spinacia oleracea) leaves, chloroplasts, and purified light-harvesting complexes. The characteristic biphasic pattern of fluorescence quenching in dark-adapted leaves, which was removed by preillumination, was evidence of light activation of qN, a process correlated with the de-epoxidation state of the xanthophyll cycle carotenoids. Chloroplasts isolated from dark-adapted and light-activated leaves confirmed the nature of light activation: faster and greater quenching at a subsaturating transthylakoid pH gradient. The light-harvesting chlorophyll a/b-binding complexes of photosystem II were isolated from dark-adapted and light-activated leaves. When isolated from light-activated leaves, these complexes showed an increase in the rate of quenching in vitro compared with samples prepared from dark-adapted leaves. In all cases, the quenching kinetics were fitted to a single component hyperbolic function. For leaves, chloroplasts, and light-harvesting complexes, the presence of zeaxanthin was associated with an increased rate constant for the induction of quenching. We discuss the significance of these observations in terms of the mechanism and control of qN.

Advances in random matrix theory, zeta functions, and sphere packing

Over four hundred years ago, Sir Walter Raleigh asked his mathematical assistant to find formulas for the number of cannonballs in regularly stacked piles. These investigations aroused the curiosity of the astronomer Johannes Kepler and led to a problem that has gone centuries without a solution: why is the familiar cannonball stack the most efficient arrangement possible? Here we discuss the solution that Hales found in 1998. Almost every part of the 282-page proof relies on long computer verifications. Random matrix theory was developed by physicists to describe the spectra of complex nuclei. In particular, the statistical fluctuations of the eigenvalues (“the energy levels”) follow certain universal laws based on symmetry types. We describe these and then discuss the remarkable appearance of these laws for zeros of the Riemann zeta function (which is the generating function for prime numbers and is the last special function from the last century that is not understood today.) Explaining this phenomenon is a central problem. These topics are distinct, so we present them separately with their own introductory remarks.

Direct searches for dark matter: Recent results

There is abundant evidence for large amounts of unseen matter in the universe. This dark matter, by its very nature, couples feebly to ordinary matter and is correspondingly difficult to detect. Nonetheless, several experiments are now underway with the sensitivity required to detect directly galactic halo dark matter through their interactions with matter and radiation. These experiments divide into two broad classes: searches for weakly interacting massive particles (WIMPs) and searches for axions. There exists a very strong theoretical bias for supposing that supersymmetry (SUSY) is a correct description of nature. WIMPs are predicted by this SUSY theory and have the required properties to be dark matter. These WIMPs are detected from the byproducts of their occasional recoil against nucleons. There are efforts around the world to detect these rare recoils. The WIMP part of this overview focuses on the cryogenic dark matter search (CDMS) underway in California. Axions, another favored dark matter candidate, are predicted to arise from a minimal extension of the standard model that explains the absence of the expected large CP violating effects in strong interactions. Axions can, in the presence of a large magnetic field, turn into microwave photons. It is the slight excess of photons above noise that signals the axion. Axion searches are underway in California and Japan. The axion part of this overview focuses on the California effort. Brevity does not allow me to discuss other WIMP and axion searches, likewise for accelerator and satellite based searches; I apologize for their omission.

Symmetry and the energy landscapes of biomolecules

The role of symmetry in the folding of proteins is discussed using energy landscape theory. An analytical argument shows it is much easier to find sequences with funneled energy landscape capable of fast folding if the structure is symmetric. The analogy with phase transitions of small clusters with magic numbers is discussed.

Unifying theory of hypoxia tolerance: molecular/metabolic defense and rescue mechanisms for surviving oxygen lack.

We develop a unifying theory of hypoxia tolerance based on information from two cell level models (brain cortical cells and isolated hepatocytes) from the highly anoxia tolerant aquatic turtle and from other more hypoxia sensitive systems. We propose that the response of hypoxia tolerant systems to oxygen lack occurs in two phases (defense and rescue). The first lines of defense against hypoxia include a balanced suppression of ATP-demand and ATP-supply pathways; this regulation stabilizes (adenylates) at new steady-state levels even while ATP turnover rates greatly decline. The ATP demands of ion pumping are down-regulated by generalized "channel" arrest in hepatocytes and by "spike" arrest in neurons. Hypoxic ATP demands of protein synthesis are down-regulated probably by translational arrest. In hypoxia sensitive cells this translational arrest seems irreversible, but hypoxia-tolerant systems activate "rescue" mechanisms if the period of oxygen lack is extended by preferentially regulating the expression of several proteins. In these cells, a cascade of processes underpinning hypoxia rescue and defense begins with an oxygen sensor (a heme protein) and a signal-transduction pathway, which leads to significant gene-based metabolic reprogramming-the rescue process-with maintained down-regulation of energy-demand and energy-supply pathways in metabolism throughout the hypoxic period. This recent work begins to clarify how normoxic maintenance ATP turnover rates can be drastically (10-fold) down-regulated to a new hypometabolic steady state, which is prerequisite for surviving prolonged hypoxia or anoxia. The implications of these developments are extensive in biology and medicine.

Quantum theory of spin waves in finite chiral spin chains

We calculate the effect of spin waves on the properties of finite-size spin chains with a chiral spin ground state observed on biatomic Fe chains deposited on iridium(001). The system is described with a Heisenberg model supplemented with a Dzyaloshinskii-Moriya coupling and a uniaxial single ion anisotropy that presents a chiral spin ground state. Spin waves are studied using the Holstein-Primakoff boson representation of spin operators. Both the renormalized ground state and the elementary excitations are found by means of Bogoliubov transformation, as a function of the two variables that can be controlled experimentally, the applied magnetic field and the chain length. Three main results are found. First, because of the noncollinear nature of the classical ground state, there is a significant zero-point reduction of the ground-state magnetization of the spin spiral. Second, there is a critical external field from which the ground state changes from chiral spin ground state to collinear ferromagnetic order. The character of the two lowest-energy spin waves changes from edge modes to confined bulk modes over this critical field. Third, in the spin-spiral state, the spin-wave spectrum exhibits oscillatory behavior as function of the chain length with the same period of the spin helix.

Socio-technical transitions and policy change - Advocacy coalitions in Swiss energy policy

Policies and politics are an integral part of socio-technical transitions but have not received much attention in the transitions literature so far. Drawing on the advocacy coalition framework, our paper addresses this gap with a study on actors and coalitions in Swiss energy policy. Our results show that advocacy coalitions in Switzerland have largely remained stable despite the Fukushima shock. However, heterogeneity of beliefs has increased and in 2013, even a majority of actors expressed their support for the energy transition – an indication that major policy change might be ahead. It seems that in socio-technical transitions, changes in the policy issue and in the actor base also work toward policy change, next to changes in core beliefs. We make suggestions how the advocacy coalition framework can inform analysis and theory building in transition studies. We also present first ideas about the interplay of socio-technical systems and policy systems.

The young woman's companion, or, Frugal housewife : containing the most approved methods of pickling, preserving, potting, collaring, confectionary, managing and colouring foreign wines and spirits, making English wines, compounds, &c., &c. : also, the art of cookery containing directions for dressing all kinds of butchers' meat, poultry, game, fish, &c., &c. : with the complete art of carving, illustrated and made plain by engravings : likewise instructions for marketing : with the theory of brewing malt liquor : to which are added directions for letter writing, drawing, painting, &c., and several valuable miscellaneous pieces.

Includes index

The energy transport properties of one dimensional anharmonic lattices.

Vita.

Theory and methods of magnet systems design : a senior thesis /

"AEC Contract AT930-1)-2137."

Preliminary memorandum on the Dark Horse and Saturday areas, Marysvale, Utah /

"Contract no. AT-(30-1)-702"--Page ii.

Neutron slowing down in group diffusion theory

"Contract AT-11-1-GEN-14. Bettis PLant, Pittsburgh, Pa., operated for the U. S. Atomic Energy Commission by Westinghouse Electric Corporation."