Dynamical fluctuations in biochemical reactions and cycles

We develop theory for the dynamics and fluctuations in some cyclic and linear biochemical reactions. We use the approach of maximum caliber, which computes the ensemble of paths taken by the system, given a few experimental observables. This approach may be useful for interpreting single-molecule or few-particle experiments on molecular motors, enzyme reactions, ion-channels, and phosphorylation-driven biological clocks. We consider cycles where all biochemical states are observable. Our method shows how: (1) the noise in cycles increases with cycle size and decreases with the driving force that spins the cycle and (2) provides a recipe for estimating small-number features, such as probability of backward spin in small cycles, from experimental data. The back-spin probability diminishes exponentially with the deviation from equilibrium. We believe this method may also be useful for other few-particle nonequilibrium biochemical reaction systems

Secondary Structures in Long Compact Polymers

Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte-Carlo algorithm which uniformly samples compact polymer configurations in an efficient manner allowing investigations of chains much longer than previously studied. Chain configurations generated by the algorithm are used to compute statistics of secondary structures in compact polymers. We determine the fraction of monomers participating in secondary structures, and show that it is self averaging in the long chain limit and strictly less than one. Comparison with results for lattice models of open polymer chains shows that compact chains are significantly more likely to form secondary structure.Comment: 14 pages, 14 figure

Cryostatless high temperature supercurrent bearings for rocket engine turbopumps

The rocket engine systems examined include SSME, ALS, and CTV systems. The liquid hydrogen turbopumps in the SSME and ALS vehicle systems are identified as potentially attractive candidates for development of Supercurrent Bearings since the temperatures around the bearings is about 30 K, which is considerably lower than the 95 K transition temperatures of HTS materials. At these temperatures, the current HTS materials are shown to be capable of developing significantly higher current densities. This higher current density capability makes the development of supercurrent bearings for rocket engines an attractive proposition. These supercurrent bearings are also shown to offer significant advantages over conventional bearings used in rocket engines. They can increase the life and reliability over rolling element bearings because of noncontact operation. They offer lower power loss over conventional fluid film bearings. Compared to conventional magnetic bearings, they can reduce the weight of controllers significantly, and require lower power because of the use of persistent currents. In addition, four technology areas that require further attention have been identified. These are: Supercurrent Bearing Conceptual Design Verification; HTS Magnet Fabrication and Testing; Cryosensors and Controller Development; and Rocket Engine Environmental Compatibility Testing

Magnetic suspension characteristics of electromagnetic actuators

Electromagnetic actuators that use a current-carrying coil (which is placed in a magnetic field) to generate mechanical force are conceptually attractive components for active control of rotating shafts. In one concept that is being tested in the laboratory, the control forces from such actuators are applied on the flexibly supported bearing housings of the rotor. Development of this concept into a practical reality requires a clear and thorough understanding of the role of electromechanical parameters of these actuators in delivering the right amount of control force at the right phase into the rotor. The electromechanical parameters of the actuators investigated are the mass of the armature, stiffness of its suspension, electrical resistance, and inductance of the coils. Improper selection of these parameters can result in degradation in their performance, leading to mistuning between the actuator and the rotor. Through a simple analysis, it is shown that use of such mistuned actuators could result in sharp fluctuations in the phase of the control force delivered into the rotor around the critical speeds. These sharp fluctuations in phase, called 'Phase Glitches', are undesirable. Hence, future designs of controllers should take into account the undesirable mistuning effects between the actuator and the rotor caused by the phase glitches

Solvation vs. freezing in a heteropolymer globule

We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed configurations by a Gaussian distribution of energy levels, whose mean and variance depend on the set's composition. Within such a random energy model, mean surface composition is proportional to solvation strength under most conditions. The breadth of this linear response regime arises from approximate statistical independence of surface and volume energies. For a diverse set of monomer types, the excess of solvophilic monomers at the surface is large only for very strong solvent preference, even in the ground state.Comment: 10 pages, 1 figur

Unbiased sampling of globular lattice proteins in three dimensions

We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64^3 = 262144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system

Evolution of the potential-energy surface of amorphous silicon

The link between the energy surface of bulk systems and their dynamical properties is generally difficult to establish. Using the activation-relaxation technique (ART nouveau), we follow the change in the barrier distribution of a model of amorphous silicon as a function of the degree of relaxation. We find that while the barrier-height distribution, calculated from the initial minimum, is a unique function that depends only on the level of distribution, the reverse-barrier height distribution, calculated from the final state, is independent of the relaxation, following a different function. Moreover, the resulting gained or released energy distribution is a simple convolution of these two distributions indicating that the activation and relaxation parts of a the elementary relaxation mechanism are completely independent. This characterized energy landscape can be used to explain nano-calorimetry measurements.Comment: 5 pages, 4 figure

Nonuniversal power law scaling in the probability distribution of scientific citations

We develop a model for the distribution of scientific citations. The model involves a dual mechanism: in the direct mechanism, the author of a new paper finds an old paper A and cites it. In the indirect mechanism, the author of a new paper finds an old paper A only via the reference list of a newer intermediary paper B, which has previously cited A. By comparison to citation databases, we find that papers having few citations are cited mainly by the direct mechanism. Papers already having many citations ('classics') are cited mainly by the indirect mechanism. The indirect mechanism gives a power-law tail. The 'tipping point' at which a paper becomes a classic is about 21 citations for papers published in the Institute for Scientific Information (ISI) Web of Science database in 1981, 29 for Physical Review D papers published from 1975-1994, and 39 for all publications from a list of high h-index chemists assembled in 2007. The power-law exponent is not universal. Individuals who are highly cited have a systematically smaller exponent than individuals who are less cited.Comment: 7 pages, 3 figures, 2 table