Capillarity Theory for the Fly-Casting Mechanism

Biomolecular folding and function are often coupled. During molecular recognition events, one of the binding partners may transiently or partially unfold, allowing more rapid access to a binding site. We describe a simple model for this flycasting mechanism based on the capillarity approximation and polymer chain statistics. The model shows that flycasting is most effective when the protein unfolding barrier is small and the part of the chain which extends towards the target is relatively rigid. These features are often seen in known examples of flycasting in protein-DNA binding. Simulations of protein-DNA binding based on well-funneled native-topology models with electrostatic forces confirm the trends of the analytical theory

Magnetoresistance due to Domain Walls in Micron Scale Fe Wires with Stripe Domains

The magnetoresistance (MR) associated with domain boundaries has been investigated in microfabricated bcc Fe (0.65 to 20 $\mu$m linewidth) wires with controlled stripe domains. Domain configurations have been characterized using magnetic force microscopy. MR measurements as a function of field angle, temperature and domain configuration are used to estimate MR contributions due to resistivity anisotropy and domain walls. Evidence is presented that domain boundaries enhance the conductivity in such microstructures over a broad range of temperatures (1.5 K to 80 K).Comment: 8 pages, 3 postscript figures, and 2 jpg images (Fig 1 and 2) to appear in IEEE Transactions on Magnetics (Fall 1998

Fe-doping-induced evolution of charge-orbital ordering in a bicritical-state manganite

Impurity effects on the stability of a ferromagnetic metallic state in a bicritical-state manganite, (La0.7Pr0.3)0.65Ca0.35MnO3, on the verge of metal-insulator transition have been investigated by substituting a variety of transition-metal atoms for Mn ones. Among them, Fe doping exhibits the exceptional ability to dramatically decrease the ferromagnetic transition temperature. Systematic studies on the magnetotransport properties and x-ray diffraction for the Fe-doped crystals have revealed that charge-orbital ordering evolves down to low temperatures, which strongly suppresses the ferromagnetic metallic state. The observed glassy magnetic and transport properties as well as diffuse phase transition can be attributed to the phase-separated state where short-range charge-orbital-ordered clusters are embedded in the ferromagnetic metallic matrix. Such a behavior in the Fe-doped manganites form a marked contrast to the Cr-doping effects on charge-orbital-ordered manganites known as impurity-induced collapse of charge-orbital ordering.Comment: 8 pages, 7 figure

A Few More Examples May Be Worth Billions of Parameters

We investigate the dynamics of increasing the number of model parameters versus the number of labeled examples across a wide variety of tasks. Our exploration reveals that while scaling parameters consistently yields performance improvements, the contribution of additional examples highly depends on the task's format. Specifically, in open question answering tasks, enlarging the training set does not improve performance. In contrast, classification, extractive question answering, and multiple choice tasks benefit so much from additional examples that collecting a few hundred examples is often “worth” billions of parameters. We hypothesize that unlike open question answering, which involves recalling specific information, solving strategies for tasks with a more restricted output space transfer across examples, and can therefore be learned with small amounts of labeled data

A Closer Look at the Performance of Neural Language Models on Reflexive Anaphor Licensing

An emerging line of work uses psycholinguistic methods to evaluate the syntactic generalizations acquired by neural language models (NLMs). While this approach has shown NLMs to be capable of learning a wide range of linguistic knowledge, confounds in the design of previous experiments may have obscured the potential of NLMs to learn certain grammatical phenomena. Here we re-evaluate the performance of a range of NLMs on reflexive anaphor licensing. Under our paradigm, the models consistently show stronger evidence of learning than reported in previous work. Our approach demonstrates the value of well-controlled psycholinguistic methods in gaining a fine-grained understanding of NLM learning potential

Evidences of a consolute critical point in the Phase Separation regime of La(5/8-y)Pr(y)Ca(3/8)MnO(3) (y = 0.4) single crystals

We report on DC and pulsed electric field sensitivity of the resistance of mixed valent Mn oxide based La(5/8-y)Pr(y)Ca(3/8)MnO(3) (y = 0.4) single crystals as a function of temperature. The low temperature regime of the resistivity is highly current and voltage dependent. An irreversible transition from high (HR) to a low resistivity (LR) is obtained upon the increase of the electric field up to a temperature dependent critical value (V_c). The current-voltage characteristics in the LR regime as well as the lack of a variation in the magnetization response when V_c is reached indicate the formation of a non-single connected filamentary conducting path. The temperature dependence of V_c indicates the existence of a consolute point where the conducting and insulating phases produce a critical behavior as a consequence of their separation.Comment: 5 pages, 6 figures, corresponding author: C. Acha ([email protected]

Zero Temperature Phase Transition in Spin-ladders: Phase Diagram and Dynamical studies of Cu(Hp)Cl

In a magnetic field, spin-ladders undergo two zero-temperature phase transitions at the critical fields Hc1 and Hc2. An experimental review of static and dynamical properties of spin-ladders close to these critical points is presented. The scaling functions, universal to all quantum critical points in one-dimension, are extracted from (a) the thermodynamic quantities (magnetization) and (b) the dynamical functions (NMR relaxation). A simple mapping of strongly coupled spin ladders in a magnetic field on the exactly solvable XXZ model enables to make detailed fits and gives an overall understanding of a broad class of quantum magnets in their gapless phase (between Hc1 and Hc2). In this phase, the low temperature divergence of the NMR relaxation demonstrates its Luttinger liquid nature as well as the novel quantum critical regime at higher temperature. The general behaviour close these quantum critical points can be tied to known models of quantum magnetism.Comment: few corrections made, 15 pages, to be published in European Journal of Physics

Phonon Thermal Transport of URu2Si2: Broken Translational Symmetry and Strong-Coupling of the Hidden Order to the Lattice

A dramatic increase in the total thermal conductivity (k) is observed in the Hidden Order (HO) state of single crystal URu2Si2. Through measurements of the thermal Hall conductivity, we explicitly show that the electronic contribution to k is extremely small, so that this large increase in k is dominated by phonon conduction. An itinerant BCS/mean-field model describes this behavior well: the increase in kappa is associated with the opening of a large energy gap at the Fermi Surface, thereby decreasing electron-phonon scattering. Our analysis implies that the Hidden Order parameter is strongly coupled to the lattice, suggestive of a broken symmetry involving charge degrees of freedom.Comment: 17 pages including figures, updated author institutions and acknowledgement

Confinement Effects on the Kinetics and Thermodynamics of Protein Dimerization

In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the interplay of these effects in the crowded cellular environment? We study dimerization of a model homodimer both when the mondimers are free or tethered to each other. We consider a structured environment: Two monomers first diffuse into a cavity of size $L$ and then fold and bind within the cavity. The folding and binding are simulated using molecular dynamics based on a simplified topology based model. The {\it confinement} in the cell is described by an effective molecular concentration $C \sim L^{-3}$. A two-state coupled folding and binding behavior is found. We show the maximal rate of dimerization occurred at an effective molecular concentration $C^{op}\simeq 1m$M which is a relevant cellular concentration. In contrast, for tethered chains the rate keeps at a plateau when $CC^{op}$. For both the free and tethered cases, the simulated variation of the rate of dimerization and thermodynamic stability with effective molecular concentration agrees well with experimental observations. In addition, a theoretical argument for the effects of confinement on dimerization is also made