611 research outputs found
Theoretical Perspectives on Protein Folding
Understanding how monomeric proteins fold under in vitro conditions is
crucial to describing their functions in the cellular context. Significant
advances both in theory and experiments have resulted in a conceptual framework
for describing the folding mechanisms of globular proteins. The experimental
data and theoretical methods have revealed the multifaceted character of
proteins. Proteins exhibit universal features that can be determined using only
the number of amino acid residues (N) and polymer concepts. The sizes of
proteins in the denatured and folded states, cooperativity of the folding
transition, dispersions in the melting temperatures at the residue level, and
time scales of folding are to a large extent determined by N. The consequences
of finite N especially on how individual residues order upon folding depends on
the topology of the folded states. Such intricate details can be predicted
using the Molecular Transfer Model that combines simulations with measured
transfer free energies of protein building blocks from water to the desired
concentration of the denaturant. By watching one molecule fold at a time, using
single molecule methods, the validity of the theoretically anticipated
heterogeneity in the folding routes, and the N-dependent time scales for the
three stages in the approach to the native state have been established. Despite
the successes of theory, of which only a few examples are documented here, we
conclude that much remains to be done to solve the "protein folding problem" in
the broadest sense.Comment: 48 pages, 9 figure
Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing
We show that Kramers rate theory gives a straightforward, accurate estimate
of the closing time of a semiflexible polymer that is valid in cases
of physical interest. The calculation also reveals how the time scales of chain
relaxation and closing are intertwined, illuminating an apparent conflict
between two ways of calculating in the flexible limit.Comment: Europhys. Lett., 2003 (in press). 8 pages, 3 figures. See also,
physics/0101087 for physicist's approach to and the importance of
semiflexible polymer looping, in DNA replicatio
Viscosity Dependence of the Folding Rates of Proteins
The viscosity dependence of the folding rates for four sequences (the native
state of three sequences is a beta-sheet, while the fourth forms an
alpha-helix) is calculated for off-lattice models of proteins. Assuming that
the dynamics is given by the Langevin equation we show that the folding rates
increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and
have a maximum at intermediate values. The Kramers theory of barrier crossing
provides a quantitative fit of the numerical results. By mapping the simulation
results to real proteins we estimate that for optimized sequences the time
scale for forming a four turn \alpha-helix topology is about 500 nanoseconds,
whereas the time scale for forming a beta-sheet topology is about 10
microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at
http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical
Review Letter
Magnetic field stabilization system for atomic physics experiments
Atomic physics experiments commonly use millitesla-scale magnetic fields to
provide a quantization axis. As atomic transition frequencies depend on the
amplitude of this field, many experiments require a stable absolute field. Most
setups use electromagnets, which require a power supply stability not usually
met by commercially available units. We demonstrate stabilization of a field of
14.6 mT to 4.3 nT rms noise (0.29 ppm), compared to noise of 100 nT
without any stabilization. The rms noise is measured using a field-dependent
hyperfine transition in a single Ca ion held in a Paul trap at the
centre of the magnetic field coils. For the Ca "atomic clock" qubit
transition at 14.6 mT, which depends on the field only in second order, this
would yield a projected coherence time of many hours. Our system consists of a
feedback loop and a feedforward circuit that control the current through the
field coils and could easily be adapted to other field amplitudes, making it
suitable for other applications such as neutral atom traps.Comment: 6 pages, 5 figure
Comprehensive review of various corrosion behaviours on 316 stainless steel
Corrosion is a destructive process that converts the pure metal into a chemically stabled form by hydroxide or sulphide and it is a slow process of destruction on the material by the chemical or electrochemical reaction in the environmental space. This kind of destruction has been typically produced from oxides or salt content on the material and it results in distinctive orange coloration. The classifications of corrosion act on atmospheric air and liquids as well as on contact of two solids. To resist the corrosion rate, stainless steel 316 has been chosen because of the presence of 2-3% molybdenum content and the presence of molybdenum plays a vital role in corrosion resistance. In this study, literature related to various works has been reviewed to explain the corrosion behaviour on cavitation, crevice, electrochemical, erosion, fatigue, galvanic, uniform, pitting, and stress corrosion which act on 316 stainless steel. In the present work, several coating processes and the additives, that have been added to SS 316 to enhance the outcomes according to various corrosion causes, are discussed
High-rate, high-fidelity entanglement of qubits across an elementary quantum network
We demonstrate remote entanglement of trapped-ion qubits via a
quantum-optical fiber link with fidelity and rate approaching those of local
operations. Two Sr qubits are entangled via the polarization
degree of freedom of two photons which are coupled by high-numerical-aperture
lenses into single-mode optical fibers and interfere on a beamsplitter. A novel
geometry allows high-efficiency photon collection while maintaining unit
fidelity for ion-photon entanglement. We generate remote Bell pairs with
fidelity at an average rate (success
probability ).Comment: v2 updated to include responses to reviewers, as published in PR
Fractal Analysis of Protein Potential Energy Landscapes
The fractal properties of the total potential energy V as a function of time
t are studied for a number of systems, including realistic models of proteins
(PPT, BPTI and myoglobin). The fractal dimension of V(t), characterized by the
exponent \gamma, is almost independent of temperature and increases with time,
more slowly the larger the protein. Perhaps the most striking observation of
this study is the apparent universality of the fractal dimension, which depends
only weakly on the type of molecular system. We explain this behavior by
assuming that fractality is caused by a self-generated dynamical noise, a
consequence of intermode coupling due to anharmonicity. Global topological
features of the potential energy landscape are found to have little effect on
the observed fractal behavior.Comment: 17 pages, single spaced, including 12 figure
Semiflexible chains in confined spaces
We develop an analytical method for studying the properties of a noninteracting wormlike chain (WLC) in confined geometries. The mean-field-like theory replaces the rigid constraints of confinement with average constraints, thus allowing us to develop a tractable method for treating a WLC wrapped on the surface of a sphere, and fully encapsulated within it. The efficacy of the theory is established by reproducing the exact correlation functions for a WLC confined to the surface of a sphere. In addition, the coefficients in the free energy are exactly calculated. We also describe the behavior of a surface-confined chain under external tension that is relevant for single molecule experiments on histone-DNA complexes. The force-extension curves display spatial oscillations, and the extension of the chain, whose maximum value is bounded by the sphere diameter, scales as f−1 at large forces, in contrast to the unconfined chain that approaches the contour length as f−1∕2. A WLC encapsulated in a sphere, that is relevant for the study of the viral encapsulation of DNA, can also be treated using the mean-field approach. The predictions of the theory for various correlation functions are in excellent agreement with Langevin simulations. We find that strongly confined chains are highly structured by examining the correlations using a local winding axis. The predicted pressure of the system is in excellent agreement with simulations but, as is known, is significantly lower than the pressures seen for DNA packaged in viral capsids
Relaxational behavior of the infinite-range Ising spin-glass in a transverse field
We study the zero-temperature behavior of the infinite-ranged Ising spin
glass in a transverse field. Using spin summation techniques and Monte Carlo
methods we characterize the zero-temperature quantum transition. Our results
are well compatible with a value for the correlation length
exponent, for the dynamical exponent and an algebraic decay for
the imaginary-time correlation function. The zero-temperature relaxation of the
energy in the presence of the transverse field shows that the system
monotonically reaches the ground state energy due to tunneling processes and
displays strong glassy effects.Comment: 15 pages + 5 Figures, Revte
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