Valid and efficient formula for free energy difference from nonequilibrium work

Atomic force microscopes and optical tweezers afford direct probe into the inner working of single biomolecules by mechanically unfolding them.^1-15^ Critical to the success of this type of probe is to correctly extract the free energy differences between the various conformations of a protein/nucleic acid along its forced unfolding pathways. Current studies rely on the Jarzynski equality^16^ (JE) or its undergirding Crooks fluctuation theorem^17^ (CFT), even though questions remain on its validity^17-19^ and on its accuracy.^13,20-21^ The validity of JE relies on the assumption of microscopic reversibility.^17,18^ The dynamics of biomolecules, however, is Langevin stochastic in nature. The frictional force in the Langevin equation breaks the time reversal symmetry and renders the dynamics microscopically irreversible even though detailed balance holds true. The inaccuracy of JE has largely been attributed to the fact that one cannot sample a large enough number of unfolding paths in a given study, experimental or computational.^13,15^ Here I show that both of these questions can be answered with a new equation relating the nonequilibrium work to the equilibrium free energy difference. The validity of this new equation requires detailed balance but not microscopic reversibility. Taking into the new equation equal number of unfolding and refolding paths, the accuracy is enhanced ten folds in comparison to a JE study based on a similar but larger number of unfolding paths

Glycerol Modulates Water Permeation through Escherichia coli Aquaglyceroporin GlpF

Among aquaglyceroporins that transport both water and glycerol across the cell membrane, Escherichia coli glycerol uptake facilitator (GlpF) is the most thoroughly studied. However, one question remains: Does glycerol modulate water permeation? This study answers this fundamental question by determining the chemical-potential profile of glycerol along the permeation path through GlpF's conducting pore. There is a deep well near the Asn-Pro-Ala (NPA) motifs (dissociation constant 14 microM) and a barrier near the selectivity filter (10.1 kcal/mol above the well bottom). This profile owes its existence to GlpF's perfect steric arrangement: The glycerol-protein van der Waals interactions are attractive near the NPA but repulsive elsewhere in the conducting pore. In light of the single-file nature of waters and glycerols lining up in GlpF's amphipathic pore, it leads to the following conclusion: Glycerol modulates water permeation in the microM range. At mM concentrations, GlpF is glycerol-saturated and a glycerol dwelling in the well occludes the conducting pore. Therefore, water permeation is fully correlated to glycerol dissociation that has an Arrhenius activation barrier of 6.5 kcal/mol. Validation of this theory is based on the existent in vitro data, some of which have not been given the proper attention they deserved: The Arrhenius activation barriers were found to be 7 kcal/mol for water permeation and 9.6 kcal/mol for glycerol permeation; The presence of up to 100 mM glycerol did not affect the kinetics of water transport with very low permeability, in apparent contradiction with the existent theories that predicted high permeability (0 M glycerol)

Some Issues in a Gauge Model of Unparticles

We address in a recent gauge model of unparticles the issues that are important for consistency of a gauge theory, i.e., unitarity and Ward identity of physical amplitudes. We find that non-integrable singularities arise in physical quantities like cross section and decay rate from gauge interactions of unparticles. We also show that Ward identity is violated due to the lack of a dispersion relation for charged unparticles although the Ward-Takahashi identity for general Green functions is incorporated in the model. A previous observation that the unparticle's (with scaling dimension d) contribution to the gauge boson self-energy is a factor (2-d) of the particle's has been extended to the Green function of triple gauge bosons. This (2-d) rule may be generally true for any point Green functions of gauge bosons. This implies that the model would be trivial even as one that mimics certain dynamical effects on gauge bosons in which unparticles serve as an interpolating field.Comment: v1:16 pages, 3 figures. v2: some clarifications made and presentation improved, calculation and conclusion not modified; refs added and updated. Version to appear in EPJ

Modulation efficiency of LiNbO₃ waveguide electro-optic intensity modulator operating at high microwave frequency

The modulation efficiency, at high-frequency microwave modulation, of a LiNbO3 waveguide electro-optic modulator is shown to be degraded severely, especially when it is used as a frequency translator in a Brillouin-distributed fiber-sensing system. We derive an analytical expression for this attenuation regarding the phase-velocity mismatch and the impedance mismatch during the modulation process. Theoretical results are confirmed by experimental results based on a 15 Gb/s LiNbO3 optical intensity modulator

Alignment and orientation of an adsorbed dipole molecule

Half-cycle laser pulse is applied on an absorbed molecule to investigate its alignment and orientation behavior. Crossover from field-free to hindered rotation motion is observed by varying the angel of hindrance of potential well. At small hindered angle, both alignment and orientation show sinusoidal-like behavior because of the suppression of higher excited states. However, mean alignment decreases monotonically as the hindered angle is increased, while mean orientation displays a minimum point at certain hindered angle. The reason is attributed to the symmetry of wavefunction and can be explained well by analyzing the coefficients of eigenstates.Comment: 4 pages, 4 figures, to appear in Phys. Rev. B (2004

DLC2 modulates angiogenic responses in vascular endothelial cells by regulating cell attachment and migration.

Deleted in liver cancer 1 (DLC1) is a RhoGTPase activation protein-containing tumor suppressor that associates with various types of cancer. Although DLC2 shares a similar domain structure with that of DLC1, the function of DLC2 is not well characterized. Here, we describe the expression and ablation of DLC2 in mice using a reporter-knockout approach. DLC2 is expressed in several tissues and in endothelial cells (ECs) of blood vessels. Although ECs and blood vessels show no histological abnormalities and mice appear overall healthy, DLC2-mutant mice display enhanced angiogenic responses induced by matrigel and by tumor cells. Silencing of DLC2 in human ECs has reduced cell attachment, increased migration, and tube formation. These changes are rescued by silencing of RhoA, suggesting that the process is RhoA pathway dependent. These results indicate that DLC2 is not required for mouse development and normal vessel formation, but may protect mouse from unwanted angiogenesis induced by, for example, tumor cells

Bounds on Unparticles from the Higgs Sector

We study supersymmetric QCD in the conformal window as a laboratory for unparticle physics, and analyze couplings between the unparticle sector and the Higgs sector. These couplings can lead to the unparticle sector being pushed away from its scale invariant fixed point. We show that this implies that low energy experiments will not be able to see unparticle physics, and the best hope of seeing unparticles is in high energy collider experiments such as the Tevatron and the LHC. We also demonstrate how the breaking of scale invariance could be observed at these experiments.Comment: 9 pages, 3 figure