Strong Pulling Research Articles

Ab initio interactive molecular dynamics on graphical processing units (GPUs).

A virtual molecular modeling kit is developed based on GPU-enabled interactive ab initio molecular dynamics (MD). The code uses the TeraChem and VMD programs with a modified IMD interface. Optimization of the GPU accelerated TeraChem program specifically for small molecular systems is discussed, and a robust multiple time step integrator is employed to accurately integrate strong user-supplied pulling forces. Smooth and responsive visualization techniques are developed to allow interactive manipulation at minimum simulation rates below five MD steps per second. Representative calculations at the Hartree-Fock level of theory are demonstrated for molecular systems containing up to a few dozen atoms.

When maladaptive gene flow does not increase selection.

Populations receiving high maladaptive gene flow are expected to experience strong directional selection-because gene flow pulls mean phenotypes away from local fitness peaks. We tested this prediction by means of a large and replicated mark-recapture study of threespine stickleback (Gasterosteus aculeatus) in two stream populations. One of the populations (outlet) experiences high gene flow from the lake population and its morphology is correspondingly poorly adapted. The other population (inlet) experiences very low gene flow from the lake population and its morphology is correspondingly well adapted. Contrary to the above prediction, selection was not stronger in the outlet than in the inlet, a result that forced us to consider potential reasons for why maladaptive gene flow might not increase selection. Of particular interest, we show by means of a simple population genetic model that maladaptive gene flow can-under reasonable conditions-decrease the strength of directional selection. This outcome occurs when immigrants decrease mean fitness in the resident population, which decreases the strength of selection against maladapted phenotypes. We argue that this previously unrecognized effect of gene flow deserves further attention in theoretical and empirical studies.

Spatiotemporally and mechanically controlled triggering of mast cells using atomic force microscopy

Mast cells are thought to be sensitive to mechanical forces, for example, coughing in asthma or pressure in "physical urticarias." Conversion of mechanical forces to biochemical signals could potentially augment antigenic signaling. Studying the combined effects of mechanical and antigenic cues on mast cells and other hematopoietic cells has proven difficult. Here, we present an approach using a modified atomic force microscope cantilever to deliver antigenic signals to mast cells while simultaneously applying mechanical forces. We developed a strategy to concurrently record degranulation events by fluorescence microscopy during antigenic triggering. Finally, we also measured the mechanical forces generated by mast cells while antigen receptors are ligated. We showed that mast cells respond to antigen delivered by the atomic force microscopy cantilever with prompt degranulation and the generation of strong pushing and pulling forces. We did not discern any relationship between applied mechanical forces and the kinetics of degranulation. These experiments present a new method for dissecting the interactions of mechanical and biochemical cues in the signaling responses of immune cells.

Frequency cavity pulling induced by a single semiconductor quantum dot

We investigate the emission properties of a single semiconductor quantum dot deterministically coupled to a confined optical mode in the weak-coupling regime. A strong spectral pulling, broadening, and narrowing of the cavity mode emission is evidenced when changing the spectral detuning between the emitter and the cavity. These features are theoretically accounted for by considering the phonon assisted emission of the quantum dot transition. These observations highlight a regime of cavity quantum electrodynamics scarcely investigated so far, involving spectrally broad emitters.

How Cells Feel: Stochastic Model for a Molecular Mechanosensor

Understanding mechanosensitivity (i.e., how cells sense the stiffness of their environment) is very important, yet there is a fundamental difficulty in understanding its mechanism: to measure an elastic modulus one requires two points of application of force—a measuring and a reference point. The cell in contact with substrate has only one (adhesion) point to work with, and thus a new method of measurement needs to be invented. The aim of this theoretical work is to develop a self-consistent physical model for mechanosensitivity, a process by which a cell detects the mechanical stiffness of its environment (e.g., a substrate it is attached to via adhesion points) and generates an appropriate chemical signaling to remodel itself in response to this environment. The model uses the molecular mechanosensing complex of latent TGF-β attached to the adhesion point as the biomarker. We show that the underlying Brownian motion in the substrate is the reference element in the measuring process. The model produces a closed expression for the rate of release of active TGF-β, which depends on the substrate stiffness and the pulling force coming from the cell in a subtle and nontrivial way. It is consistent with basic experimental data showing an increase in signal for stiffer substrates and higher pulling forces. In addition, we find that for each cell there is a range of stiffness where a homeostatic configuration of the cell can be achieved, outside of which the cell either relaxes its cytoskeletal forces and detaches from the very weak substrate, or generates an increasingly strong pulling force through stress fibers with a positive feedback loop on very stiff substrates. In this way, the theory offers the underlying mechanism for the myofibroblast conversion in wound healing and smooth muscle cell dysfunction in cardiac disease.

The Optimization of Chain of Talents on the Development of Large Aircraft

The aviation industry is a typically high-tech industry, which rallies a large number of high-tech achievements of mankind. Its distinct features are the high investment, long period and strong pulling function to industry. The development of large aircraft has currently become an important economic development project to promote the successful combination of technology and economy. The resources of talents are an important guarantee for this industry. First, this article studies the meaning of the talents and the chain of talents, on this basis, analyzes the chain of talents by means of SWOT, further explores optimization strategies of the chain of talents in order to serve for the large aircraft design talent strategies of our country.

The Optimization of Chain of Talents on the Development of Large Aircraft

The aviation industry is a typically high-tech industry, which rallies a large number of high-tech achievements of mankind. Its distinct features are the high investment, long period and strong pulling function to industry. The development of large aircraft has currently become an important economic development project to promote the successful combination of technology and economy. The resources of talents are an important guarantee for this industry. First, this article studies the meaning of the talents and the chain of talents, on this basis, analyzes the chain of talents by means of SWOT, further explores optimization strategies of the chain of talents in order to serve for the large aircraft design talent strategies of our country.

“Across the Boundary in a Hundred Torrents”: The Changing Geography of Marine Trade Within the Great Lakes Borderland Region During the Nineteenth and Early Twentieth Centuries

This article relies primarily on customhouse records to chart the changing geography of cross-border marine commerce taking place within the Great Lakes borderland during the nineteenth and early twentieth centuries. Early on, cross-border marine trade was much more important in the lower than upper lakes, and much of this traffic was local in nature, although a few centers on both sides developed strong gravitational pulls that translated into wider commerce fields. Further integration occurred during the middle of the century when a number of factors, including the repeal of the Corn Laws and the negotiation of reciprocity, resulted in increased flows of goods between Ontario and the Great Lakes states. It was also during this period that railways began to replace boats as the primary mode of trade transportation. On the upper lakes, cross-border trade between the ports of this region and the lower lakes increased in response to the growing demand for lumber, minerals, and other resources by expanding cities and industries. Increasingly, the asymmetrical character of cross-border trade became apparent as the volume of flows favored the United States. In this context, new corridors developed as older gateways continued to prosper or decline. Specific channels of trade linking geographically proximate communities on both sides of the St. Lawrence and the lakes continued to exist, but for most of these centers, commerce via waterborne transportation faded considerably. Within the larger trade network of the Great Lakes basin, certain arteries of trade became clogged or closed up whereas others were opened.

Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase

Clp ATPases are ring-shaped AAA+ motors in the degradation pathway that perform critical actions of unfolding and translocating substrate proteins (SPs) through narrow pores to deliver them to peptidase components. These actions are effected by conserved diaphragm-forming loops found in the central channel of the Clp ATPase hexamer. Conformational changes, that take place in the course of repetitive ATP-driven cycles, result in mechanical forces applied by the central channel loops onto the SP. We use coarse-grained simulations to elucidate allostery-driven mechanisms of unfolding and translocation of a tagged four-helix bundle protein by the ClpY ATPase. Unfolding is initiated at the tagged C-terminal region via an obligatory intermediate. The resulting nonnative conformation is competent for translocation, which proceeds on a different time scale than unfolding and involves sharp stepped transitions. Completion of the translocation process requires assistance from the ClpQ peptidase. These mechanisms contrast nonallosteric mechanical unfolding of the SP. In atomic force microscopy experiments, multiple unfolding pathways are available and large mechanical forces are required to unravel the SP relative to those exerted by the central channel loops of ClpY. SP threading through a nonallosteric ClpY nanopore involves simultaneous unfolding and translocation effected by strong pulling forces.

Structural Kinetics of Cardiac Troponin C Mutants Linked to Familial Hypertrophic and Dilated Cardiomyopathy in Troponin Complexes

The key events in regulating cardiac muscle contraction involve Ca(2+) binding to and release from cTnC (troponin C) and structural changes in cTnC and other thin filament proteins triggered by Ca(2+) movement. Single mutations L29Q and G159D in human cTnC have been reported to associate with familial hypertrophic and dilated cardiomyopathy, respectively. We have examined the effects of these individual mutations on structural transitions in the regulatory N-domain of cTnC triggered by Ca(2+) binding and dissociation. This study was carried out with a double mutant or triple mutants of cTnC, reconstituted into troponin with tryptophanless cTnI and cTnT. The double mutant, cTnC(L12W/N51C) labeled with 1,5-IAEDANS at Cys-51, served as a control to monitor Ca(2+)-induced opening and closing of the N-domain by Förster resonance energy transfer (FRET). The triple mutants contained both L12W and N51C labeled with 1,5-IAEDANS, and either L29Q or G159D. Both mutations had minimal effects on the equilibrium distance between Trp-12 and Cys-51-AEDANS in the absence or presence of bound Ca(2+). L29Q had no effect on the closing rate of the N-domain triggered by release of Ca(2+), but reduced the Ca(2+)-induced opening rate. G159D reduced both the closing and opening rates. Previous results showed that the closing rate of cTnC N-domain triggered by Ca(2+) dissociation was substantially enhanced by PKA phosphorylation of cTnI. This rate enhancement was abolished by L29Q or G159D. These mutations alter the kinetics of structural transitions in the regulatory N-domain of cTnC that are involved in either activation (L29Q) or deactivation (G159D). Both mutations appear to be antagonistic toward phosphorylation signaling between cTnI and cTnC.

Ferroelectric Domain Breakdown

A new phenomenon—ferroelectric domain breakdown, or the formation of string-like domains—is observed in various bulk ferroelectric crystals under a high inhomogeneous electric field generated at the tip of a high-voltage atomic force microscope. The domains have a high aspect ratio when their length exceeds their lateral size by two or three orders of magnitude. This chapter reviews some of the recent advances in understanding the nature of this phenomenon. The main driving force for ferroelectric domain breakdown is not the tip's electric field, which is negligibly weak near the apex of the long domain, but rather internal forces generated owing to the minimization of depolarization field energy when the domain elongates. Domain breakdown is considered an extreme manifestation of Coulomb instability, which is caused by repulsion of bound charges near the inverted domain apex. This instability leads to strong pulling of the domain apex into a region where the tip-induced electric field is negligibly small.

Tension dynamics in semiflexible polymers. II. Scaling solutions and applications

In part I [O. Hallatschek, preceding paper, Phys. Rev. E 75, 031905 (2007)] of this contribution, a systematic coarse-grained description of the dynamics of a weakly bending semiflexible polymer was developed. Here, we discuss analytical solutions of the established deterministic partial integro-differential equation for the spatiotemporal relaxation of the backbone tension. For prototypal experimental situations, such as the sudden application or release of a strong external pulling force, it is demonstrated that the tensile dynamics reflects the self-affine conformational fluctuation spectrum in a variety of intermediate asymptotic power laws. Detailed and explicit analytical predictions for the tension propagation and relaxation and corresponding results for common observables, such as the end-to-end distance, are obtained.

Retained Central Venous Lines in the Newborn: Report of One Case and Systematic Review of the Literature

The use of percutaneously inserted central catheters (PICCs) is an established practice in most NICUs. With the widespread use of these catheters, an increasing number of PICC complications has been reported in neonates. We present one case of a PICC retained and tethered in the vein in a very low birth weight infant, as well as a systematic review of PICC retention cases. Ten previous cases of PICC retention in neonates were found. Among those cases, the most common associated factors were coagulase-negative staphylococcus catheter colonization/bactcremia and long duration of catheterization. Occlusion was not a usefiul sign for predicting catheter retention. Once retention was established, heparin or urokinase instillations were ineffective. Although surgical exploration was sometimes required, firm, continuous traction applied to the catheter over several hours or intermittent, moderately strong pulling maneuvers were successful in 44.4 percent of the cases in which they were performed. Traction did not show major side effects. Our case provides additional support for use of traction as the initial approach in the management of this rare complication.

Molecular mechanisms of the chain diffusion between crystalline and amorphous fractions in polyethylene

We revisit the problem of the molecular mechanism of the chain diffusion between crystalline and amorphous fractions in semicrystalline polyethylene (PE). There exists a long-standing controversy on the nature of the topological point defects which diffuse along the chain stems in crystallites and shift the stems. Namely, the conformational (including gauche conformations) twist–compression (interstitial-like) and the smooth (soliton-like) twist–tension (vacancy-like) localized defects were offered for this role. However, none of the proposed models for the process could explain all the experimental facts which seemed unclear and contradictory. Moreover, it was discovered recently that in PE samples of uncommon morphology (electron beam irradiated samples, fibers and single crystals) the diffusion process has the activation energy about 3 times less than that in common melt-crystallized samples. No explanation ever followed. We have carried out molecular dynamics (MD) simulation of both the defects in a realistic model of PE crystal and obtained estimates for their formation energies and diffusion coefficients. These estimates together with analysis of available experimental data allow to solve both the problems and to propose models for molecular mechanisms of the observed diffusion processes. The agents of the ‘old’ diffusion process are the smooth twist–tension defects. Shifts in a chain stem of a crystallite in a common sample are initiated at the interface to an amorphous region through extended thermal motion of the chain stem in the amorphous region. If the motion causes a strong pull (with a twist) at the chain stem in the crystallite, such motion produces a smooth defect of twist–tension on this stem. The proposed molecular model conforms with available mechanical experiments if one accepts that the process corresponds to the most low temperature (α 1) from the α-peaks observed. The ‘new’ diffusion process results from diffusion of the conformational twist–compression defects in crystallites. The needed sequence of conformations appears near a crystallite as a result of a quick gamma process. Because the state of the semicrystalline polymer is unstable, the position of the boundary between the crystalline and disordered regions fluctuates so that segments of chains pass from disordered to crystalline state (and vice versa). The conformational defects in disordered region are captured through expansion of the crystalline region where they become stable and diffuse along the chains. Our MD estimate for the activation energy of the process E act ≤ 8.65 kcal/mol is in a good agreement with the experimental value 7 kcal/mol. The diffusion coefficients of both the defects are too high to have effect on the statistics of both of these very slow processes. Therefore the statistics of the ‘old’ process is the statistics of strong thermal pulls at chain stems in crystallites, and the statistics of the ‘new’ process is related to the statistics of fluctuations of the position of the boundaries between crystalline and disordered fractions.

TWIST AND STRETCH

WHAT HAPPENS TO A DNA molecule when you pull on it? A simple picture of DNA envisions it as a twisted or braided rope. Just as a rope lengthens when it unwinds, you might also expect that untwisted DNA would stretch. Independent teams in France and California have shown that this simplistic model isn't right at physiologically relevant forces. In fact, they have shown that DNA actually winds up tighter and shortens when small forces are applied. Vincent Croquette and coworkers at Ecole Normale Superieure, Paris, published their results in May in Physical Review Letters {2006, 96, 178102). Carlos Bustamante and coworkers at the University of California, Berkeley, reported their findings in July in Nature (DOI: 10.1038/ nature04974). The basic result—that pulling on DNA initially causes the double helix to increase its rate of twist—is certainly surprising given the prejudice many of us have that strong pulling untwists the double helix, says John F. Marko, a ...

Seedling establishment, underground kinetics, and clonal reiteration: How do Potentilla inclinata and Inula ensifolia get their multifunctional subterranean systems?

The development of a seedling into an adult plant comprises various underground processes. Time-lapse photography (TLP) makes them visible. This is documented for Potentilla inclinata (Rosaceae) and Inula ensifolia (Asteraceae). After germination, P. inclinata develops a taproot system. Contraction phenomena pull the basal part of the shoot at least 10 mm into the soil. Later, several adventitious roots are generated, and thus the root system changes to a fibrous one. This is followed by cloning without separation of the ramets. Seedlings of I. ensifolia develop a weak primary root. At an early stage, adventitious roots are formed at the leaf rosette. This fibrous root system exerts a strong pulling effect on the shoot. After one vegetation period the basis of the rosette is approx. 30 mm under the soil surface. Cloning includes the formation of many new horizontal shoots, which conquer new sites. These two examples show three functional steps common in the developmental progress of subterranean systems: (I) establishment of the seedling, (II) innovation and survival of the young plant, and (III) reiteration (cloning and dispersal). However, to accomplish these basic development steps the diversity of subterranean systems is enhanced by different organographical components. Furthermore, the development of subterranean systems is a dynamic process consisting of two kinetic processes: the vertical movement during seedling establishment, which brings the innovation buds to a safe soil position, and the horizontal movement during dispersal, which conquers new sites.

Assessing the welfare consequences of providing litter for feed-restricted broiler breeders

1. Broiler breeder females were fed restricted allocations of a standard wheat–soy ration to meet target body weights. They were housed on raised plastic slotted floors (S) or wood shavings litter (L) from hatch to 8 weeks when each pen of 12 birds was transferred to another pen in the same block in a 2 × 2 factorial experiment (LL, LS, SL and SS). Measures of bird welfare were taken at 4 weeks of age, and at 9 and 10 weeks following transfer to the new pens. 2. At 4 weeks of age, birds reared on S spent more time standing, pecking the feeder, the wall and other birds and less time pecking the floor compared with those on L. Gentle feather pecks, strong feather pecks and strong feather pulls were more common in S than L. 3. Mean body weight was higher and coefficient of variation lower in birds on L than S at the end of the experiment. Feather loss and damage scores at 10 weeks were higher for birds reared from hatch to 8 weeks on S. 4. Birds that were reared on S continued to peck more at the pen walls after transfer to new pens but there was no other carry-over effect on behaviour. Birds on S at 9 and 10 weeks pecked more at the walls and less often at the floor, and rested less often. There was more feather pecking on S than on L in the second week post transfer. 5. Tonic immobility was greater and plasma corticosterone concentrations were lower at the end of the experiment in birds on L than S at 9 and 10 weeks of age. The heterophil–lymphocyte ratio was similar between treatments at 4 weeks and after the birds were moved to a new pen. 6. The results are consistent with the view that litter and wall pecking has de-arousing properties and that this activity is re-directed foraging that diminishes the stress of feed restriction.

Forced Kramers escape in single-molecule pulling experiments

The pulling-induced rupture of noncovalent bonds is studied by the overdamped Kramers theory with full account of a time-varying barrier. Mechanic pulling reduces the energy barrier and leads to loading-rate dependence of the rupture force F(u)(F(t)). Tested against Langevin dynamics, four distinct regimes are identified, including kinetic dominant, weak pulling, strong pulling, and mechanic pulling dominant. Asymptotic analyses show that F(u) approximately ln F(t) in weak pulling regime and becomes 1-(F(u)F(c)) approximately [ln(F(t))E(b)](23) in strong pulling regime. Kinetic informations such as activation energy E(b) and critical force F(c) were extracted from pulling experiments for biotin-streptavidin complex.

Comparisons of damaging feather pecking and time budgets in male and female turkeys of a traditional breed and a genetically selected male line

Feather and skin pecking leading to feather loss and tissue damage is a welfare problem in commercial turkeys. A factorial experiment was designed to compare a line of unselected turkeys that previously did not exhibit this behaviour with a genetically selected male line with a propensity for damaging pecking. We also compared the time budgets of male and female turkeys from the two lines at 3, 6 and 9 weeks of age and at different times of the day. Damaging feather pecking occurred in 32% of male and 15% of female male line turkeys but was not observed in the traditional line. Time budgets of males and females were similar. Preening increased and resting, feeding and general pecking declined with age. Resting was higher in the afternoon than in the morning and male line turkeys were observed resting more often than traditional turkeys at 3 and 6 weeks. Traditional turkeys displayed more gentle feather pecks than male line poults at 9 weeks. Male turkeys of both lines showed more strong feather pecks and pulls at 3 weeks whereas female turkeys showed more at 9 weeks of age. The frequency of strong feather pulls recorded electronically increased with age but was not related to mortality. It is suggested that damaging feather pecking in turkeys may be the result of vigorous investigative pecking.

Pulling reptating polymers by one end: magnetophoresis in the Rubinstein-Duke model.

We consider the magnetophoresis problem within the Rubinstein-Duke model, i.e., a reptating polymer pulled by a constant field applied to a single end of a chain. Extensive density matrix renormalization calculations are presented of the drift velocity and the profile of the chain for various strengths of the driving field and chain lengths. We show that the velocities and the average densities of the stored length are well described by simple interpolating crossover formulas, derived under the assumption that the difference between the drift and curvilinear velocities vanishes for sufficiently long chains. The profiles, which describe the average shape of the reptating chain, also show such interesting features as some nonmonotonic behavior of the link densities for sufficiently strong pulling fields. We develop a description in which a distinction is made between links entering at the pulled head and at the unpulled tail. At weak fields the separation between the head zone and the tail zone meanders through the whole chain, while the probability of finding it close to the edges drops off. At strong fields the tail zone is confined to a small region close to the unpulled edge of the polymer.