The CS-US interval function in rabbit nictitating membrane response conditioning: Single vs multiple trials per conditioning session

The effect of varying trials per day conditions on the CS-US interval or interstimulus interval (ISI) function in rabbit nictitating membrane response conditioning was studied in two experiments. Experiment 1 showed that a 1250-msec ISI was more effective than a 250-msec ISI when there was 1 trial/day. Experiment 2 showed that as the number of trials per day decreased from 20 to 1, the superiority of the 250-msec ISI group over the 1250-msec ISI group declined, with a reversal at 1 trial/day. Results are interpreted in terms of the role of a hypothesized CS-elicited short-duration orienting response in CR performance.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/33837/1/0000095.pd

Pathways to folding, nucleation events and native geometry

We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e. that with more non-local contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.Comment: Accepted in J. Chem. Phy

Experimental variables in the effects of postsession injections of strychnine sulphate on a classically conditioned response

Postsession strychnine injections have been shown to retard acquisition rates of the classically conditioned nictitating membrane response (CCNMR) of rabbits trained at a CS-US interval of 1000 msec. The particular interval value employed in CCNMR acquisition was found to be important in the magnitude of the postsession strychnine effect. Strychnine Ss trained at a CS-US interval=1250 msec (nonoptimal) were significantly depressed in acquisition rates relative to saline controls, while strychnine Ss trained at a CS-US interval=250 msec (optimal) were not. Interpretations are based upon the presumed effects of CNS excitants on memory consolidation and possible neurological correlates of the CS-US interval parameter.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46356/1/213_2004_Article_BF00402096.pd

Twist and writhe dynamics of stiff filaments

This letter considers the dynamics of a stiff filament, in particular the coupling of twist and bend via writhe. The time dependence of the writhe of a filament is $W_r^2\sim L t^{1/4}$ for a linear filament and $W_r^2\sim t^{1/2} / L$ for a curved filament. Simulations are used to study the relative importance of crankshaft motion and tube like motion in twist dynamics. Fuller's theorem, and its relation with the Berry phase, is reconsidered for open filamentsComment: 7 Pages with 2 figure

Highly Designable Protein Structures and Inter Monomer Interactions

By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the interaction potential becomes larger than a critical value, the degree of designability of structures will depend on the parameters of potential. We also show that the existence of a unique ground state is highly sensitive to mutation in certain sites.Comment: 14 pages, Latex file, 3 latex and 6 eps figures are include

The Viscous Nonlinear Dynamics of Twist and Writhe

Exploiting the "natural" frame of space curves, we formulate an intrinsic dynamics of twisted elastic filaments in viscous fluids. A pair of coupled nonlinear equations describing the temporal evolution of the filament's complex curvature and twist density embodies the dynamic interplay of twist and writhe. These are used to illustrate a novel nonlinear phenomenon: ``geometric untwisting" of open filaments, whereby twisting strains relax through a transient writhing instability without performing axial rotation. This may explain certain experimentally observed motions of fibers of the bacterium B. subtilis [N.H. Mendelson, et al., J. Bacteriol. 177, 7060 (1995)].Comment: 9 pages, 4 figure

Folding of small proteins: A matter of geometry?

We review some of our recent results obtained within the scope of simple lattice models and Monte Carlo simulations that illustrate the role of native geometry in the folding kinetics of two state folders.Comment: To appear in Molecular Physic

Unzipping Dynamics of Long DNAs

The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For unzipping of 50 kilobase DNAs at less than about 1000 bases per second, thermal equilibrium-based theory applies. However, for higher unzipping velocities, rotational viscous drag creates a buildup of elastic torque to levels above kBT in the dsDNA region, causing the unzipping force to be well above or well below the equilibrium unzipping force during respectively unzipping and rezipping, in accord with recent experimental results of Thomen et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect of sequence on unzipping and rezipping, and the transient delay in buildup of the unzipping force due to the approach to the steady state.Comment: 15 pages Revtex file including 9 figure

Twirling and Whirling: Viscous Dynamics of Rotating Elastica

Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity. Competition between twist injection, twist diffusion, and writhing instabilities is described by a novel pair of coupled PDEs for twist and bend evolution. Analytical and numerical methods elucidate the twist/bend coupling and reveal two dynamical regimes separated by a Hopf bifurcation: (i) diffusion-dominated axial rotation, or twirling, and (ii) steady-state crankshafting motion, or whirling. The consequences of these phenomena for self-propulsion are investigated, and experimental tests proposed.Comment: To be published in Physical Review Letter