scholarly journals Diffusion and steady state distributions of flexible chemotactic enzymes

2020 ◽  
Vol 229 (17-18) ◽  
pp. 2791-2806
Author(s):  
Jaime Agudo-Canalejo ◽  
Ramin Golestanian
Keyword(s):  
Steady State ◽  
Conformational Changes ◽  
Exact Result ◽  
Specific Substrate ◽  
Dispersion Theory ◽  
Enhanced Diffusion ◽  
Long Time ◽  
Diffusion Enhancement ◽  
Induced Changes ◽  
Analytical Expressions

AbstractMany experiments in recent years have reported that, when exposed to their corresponding substrate, catalytic enzymes undergo enhanced diffusion as well as chemotaxis (biased motion in the direction of a substrate gradient). Among other possible mechanisms, in a number of recent works we have explored several passive mechanisms for enhanced diffusion and chemotaxis, in the sense that they require only binding and unbinding of the enzyme to the substrate rather than the catalytic reaction itself. These mechanisms rely on conformational changes of the enzyme due to binding, as well as on phoresis due to non-contact interactions between enzyme and substrate. Here, after reviewing and generalizing our previous findings, we extend them in two different ways. In the case of enhanced diffusion, we show that an exact result for the long-time diffusion coefficient of the enzyme can be obtained using generalized Taylor dispersion theory, which results in much simpler and transparent analytical expressions for the diffusion enhancement. In the case of chemotaxis, we show that the competition between phoresis and binding-induced changes in diffusion results in non-trivial steady state distributions for the enzyme, which can either accumulate in or be depleted from regions with a specific substrate concentration.

scholarly journals Impact of Deuteration and Temperature on Furan Ring Dynamics

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2889
Author(s):  
Przemyslaw Dopieralski ◽  
Iryna V. Omelchenko ◽  
Zdzislaw Latajka
Keyword(s):  
Conformational Changes ◽  
Furan Ring ◽  
Computational Studies ◽  
Significant Progress ◽  
Dynamic Simulations ◽  
Cyclic Molecules ◽  
Ring Dynamics ◽  
Different Temperatures ◽  
Long Time ◽  
Shape And Size

Despite significant progress in conformational analysis of cyclic molecules, the number of computational studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods. In present research, we have studied temperature driven conformational changes of the furan ring at three different temperatures. Additionally, the effect of deuteration on the ring dynamics is discussed; in addition, the aromaticity indices following the Bird and HOMA schemes are computed along all trajectories. Our ab initio molecular dynamic simulations revealed that deuteration has changed the furan ring dynamics and the obvious consequences; in addition, the shape and size of molecule are expected to be different.

Effects of slide-to-roll ratio and varying velocity on the lubrication performance of grease at low speed

2021 ◽  
pp. 135065012199336
Author(s):  
Yiming Han ◽  
Jing Wang ◽  
Xuyang Jin ◽  
Shanshan Wang ◽  
Rui Zhang
Keyword(s):  
Steady State ◽  
Critical Speed ◽  
Industrial Applications ◽  
Transient Effects ◽  
Disintegration Time ◽  
Low Speed ◽  
Existence Time ◽  
Pure Rolling ◽  
Lubrication Performance ◽  
Long Time

Under steady-state pure rolling conditions with low speed, the thickener fiber agglomerations can be maintained for a long time, generating a beneficial thicker film thickness. However, in industrial applications, motions with sliding or transient effects are very common for gears, rolling-element bearings or even chain drives, evaluation of the grease performance under such conditions is vital for determining the lubrication mechanism and designing new greases. In this project, optical interferometry experiments were carried out on a ball-disk test rig to study the disintegration time of the grease thickener agglomerations with the increase of the slide-to-roll ratio under steady-state and reciprocation motions. Under steady-state conditions, the thickener fiber agglomeration can exist for a while and the time becomes shorter with the increase of the slide-to-roll ratio above the critical speed. Below the critical speed, the thickener fiber can exist in the contact in the form of a quite thick film for a very long time under pure rolling conditions but that time is decreased with the increase of the slide-to-roll ratio. The introduction of the transient effect can further reduce the existence time of the thickener.

Effect of Energy and Dose on Transient-Enhanced Diffusion and Defect Microstructure in Low Energy High Dose As+ Implanted Si

1996 ◽  
Vol 438 ◽  
Author(s):  
V. Krishnamoorthy ◽  
D. Venables ◽  
K. Moeller ◽  
K. S. Jones ◽  
B. Freer
Keyword(s):  
Point Defects ◽  
Surface Recombination ◽  
High Dose ◽  
Enhanced Diffusion ◽  
Projected Range ◽  
Diffusion Enhancement ◽  
Defect Microstructures ◽  
Dose Dependent ◽  
Higher Doses ◽  
Defect Microstructure

Abstract(001) CZ silicon wafers were implanted with arsenic (As+) at energies of 10–50keV to doses of 2×1014 to 5×1015/cm2. All implants were amorphizing in nature. The samples were annealed at 700°C for 16hrs. The resultant defect microstructures were analyzed by XTEM and PTEM and the As profiles were analyzed by SIMS. The As profiles showed significantly enhanced diffusion in all of the annealed specimens. The diffusion enhancement was both energy and dose dependent. The lowest dose implant/annealed samples did not show As clustering which translated to a lack of defects at the projected range. At higher doses, however, projected range defects were clearly observed, presumably due to interstitials generated during As clustering. The extent of enhancement in diffusion and its relation to the defect microstructure is explained by a combination of factors including surface recombination of point defects, As precipitation, As clustering and end of range damage.

Interactions between sustained contractile activity and beta-adrenergic receptors in regulation of gene expression in skeletal muscles

1989 ◽  
Vol 256 (3) ◽  
pp. C506-C514 ◽  
Author(s):  
W. E. Kraus ◽  
T. S. Bernard ◽  
R. S. Williams
Keyword(s):  
Electrical Stimulation ◽  
Steady State ◽  
Oxidative Metabolism ◽  
Adrenergic Receptors ◽  
Contractile Activity ◽  
Mitochondrial Enzymes ◽  
Beta Adrenergic Receptors ◽  
Beta Adrenergic ◽  
Induced Changes ◽  
Aldolase A

Continuous electrical stimulation for 10-21 days of the motor nerve innervating the anterior compartment muscles of adult rabbits increased both the density of beta-adrenergic receptors (beta-AR) and tissue concentrations of adenosine 3',5'-cyclic monophosphate (cAMP) by two to threefold. Changes in cAMP and in beta-AR occurred in parallel with stimulation-induced adaptations in the specific activity of mitochondrial enzymes (2- to 6-fold increases) and with changes in steady-state concentrations of mitochondrial RNA, beta-F1ATPase mRNA, and myoglobin mRNA (2- to 11-fold increases). These increases in muscle cAMP, in beta-AR, and in expression of protein and mRNA products of genes encoding proteins of oxidative metabolism occurred even in animals receiving high doses of propranolol during the period of electrical stimulation. In contrast to genes that encode proteins of oxidative metabolism, the direction and the time course of activity-induced changes in expression of the glycolytic enzyme aldolase A appeared to be unrelated to changes in muscle cAMP; suppression of steady-state concentrations of aldolase A mRNA was maximal (20-25% of control) at early time points preceding the maximal rise in cAMP. In addition, administration of propranolol attenuated the suppressive effect of continuous contractile activity on expression of aldolase A, even in the absence of an effect of this drug on cAMP in stimulated muscles. We conclude that activity-induced changes in cAMP, in beta-AR, and in expression of genes that encode proteins important for oxidative metabolism occur as a direct consequence of contractile activity and do not require concomitant stimulation of beta-AR.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals NMR studies of anion-induced conformational changes in diindolylureas and diindolylthioureas

2011 ◽  
Vol 7 ◽  
pp. 1205-1214 ◽  
Author(s):  
Damjan Makuc ◽  
Jennifer R Hiscock ◽  
Mark E Light ◽  
Philip A Gale ◽  
Janez Plavec
Keyword(s):  
Conformational Changes ◽  
Chemical Shifts ◽  
Dihydrogen Phosphate ◽  
Nmr Studies ◽  
Receptor Complexes ◽  
Hydrogen Bond Interactions ◽  
Weak Binding ◽  
Oxo Anions ◽  
Induced Changes ◽  
Good Agreement

The conformational properties of 1,3-diindolylureas and thioureas were studied by a combination of heteronuclear NMR spectroscopy and quantum mechanics calculations. NOE experiments showed that the anti–anti conformer along the C7–N7α bonds was predominant in DMSO-d 6 solution in the absence of anions. Anion-induced changes in the 1H and 15N chemical shifts confirm the weak binding of chloride anions with negligible conformational changes. Strong deshielding of ureido protons and moderate deshielding of indole NH was observed upon the addition of acetate, benzoate, bicarbonate and dihydrogen phosphate, which indicated that the predominant hydrogen bond interactions occurred at the urea donor groups. Binding of oxo-anions caused conformational changes along the C7–N7α bonds and the syn–syn conformer was preferred for anion–receptor complexes. The conformational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations.

Super-Fine Structure in the Critical Flow-Rate of Critical Flow Venturi Nozzles

2002 ◽  
Author(s):  
Masahiro Ishibashi
Keyword(s):  
Fine Structure ◽  
Steady State ◽  
Discharge Coefficient ◽  
Constant Pressure ◽  
Pressure Ratio ◽  
Critical Flow ◽  
Time Intervals ◽  
Critical Flow Rate ◽  
A Value ◽  
Long Time

It is shown that critical flow Venturi nozzles need time intervals, i.e., more than five hours, to achieve steady state conditions. During these intervals, the discharge coefficient varies gradually to reach a value inherent to the pressure ratio applied. When a nozzle is suddenly put in the critical condition, its discharge coefficient is trapped at a certain value then afterwards approaches gradually to the inherent value. Primary calibrations are considered to have measured the trapped discharge coefficient, whereas nozzles in applications, where a constant pressure ratio is applied for a long time, have a discharge coefficient inherent to the pressure ratio; inherent and trapped coefficients can differ by 0.03–0.04%.

scholarly journals A theoretical verification of the integral fluctuation theorem for accelerated colloidal systems in the long-time limit

2021 ◽  
Author(s):  
Yash Lokare
Keyword(s):  
Steady State ◽  
Time Scales ◽  
Numerical Study ◽  
Quantitative Description ◽  
Experimental Studies ◽  
Fluctuation Theorem ◽  
Nonequilibrium Steady States ◽  
Small Scale ◽  
Colloidal Systems ◽  
Long Time

A quantitative description of the violation of the second law of thermodynamics in relatively small classical systems and over short time scales comes from the fluctuation-dissipation theorem. It has been well established both theoretically and experimentally, the validity of the fluctuation theorem to small scale systems that are disturbed from their initial equilibrium states. Some experimental studies in the past have also explored the validity of the fluctuation theorem to nonequilibrium steady states at long time scales in the asymptotic limit. To this end, a theoretical and/or purely numerical model of the integral fluctuation theorem has been presented. An approximate general expression for the dissipation function has been derived for accelerated colloidal systems trapped/confined in power-law traps. Thereafter, a colloidal particle trapped in a harmonic potential (generated by an accelerating one-dimensional optical trap) and undergoing Brownian motion has been considered for the numerical study. A toy model of a quartic potential trap in addition to the harmonic trap has also been considered for the numerical study. The results presented herein show that the integral fluctuation theorem applies not only to equilibrium steady state distributions but also to nonequilibrium steady state distributions of colloidal systems in accelerated frames of reference over long time scales.

TRANSMITTING BIPARTITE AND MULTIPARTITE CORRELATIONS VIA SPIN CHAINS UNDER PHASE DECOHERENCE

2012 ◽  
Vol 10 (06) ◽  
pp. 1250073
Author(s):  
JIAN-FENG AI ◽  
JIAN-SONG ZHANG ◽  
AI-XI CHEN
Keyword(s):  
Steady State ◽  
Anisotropy Parameter ◽  
Quantum Correlations ◽  
Spin Chains ◽  
The Other ◽  
Bipartite Entanglement ◽  
Other Hand ◽  
Long Time ◽  
Phase Decoherence ◽  
The One

We investigate the transfer of bipartite (measured by cocurrence) and multipartite (measured by global discord) quantum correlations though spin chains under phase decoherence. The influence of phase decoherence and anisotropy parameter upon quantum correlations transfer is investigated. On the one hand, in the case of no phase decoherence, there is no steady state quantum correlations between spins. On the other hand, if the phase decoherence is larger than zero, the bipartite quantum correlations can be transferred through a Heisenberg XXX chain for a long time and there is steady state bipartite entanglement. For a Heisenberg XX chain, bipartite entanglement between two spins is destroyed completely after a long time. Multipartite quantum correlations of all spins are more robust than bipartite quantum correlations. Thus, one can store multipartite quantum correlations in spin chains for a long time under phase decoherence.

On the analysis of the integral fluctuation theorem for accelerated colloidal systems in the long-time limit

2021 ◽  
Author(s):  
Yash Lokare
Keyword(s):  
Steady State ◽  
Time Scales ◽  
Numerical Study ◽  
Quantitative Description ◽  
Experimental Studies ◽  
Fluctuation Theorem ◽  
Nonequilibrium Steady States ◽  
Small Scale ◽  
Colloidal Systems ◽  
Long Time

Abstract A quantitative description of the violation of the second law of thermodynamics in relatively small classical systems and over short time scales comes from the fluctuation-dissipation theorem. It has been well established both theoretically and experimentally, the validity of the fluctuation theorem to small scale systems that are disturbed from their initial equilibrium states. Some experimental studies in the past have also explored the validity of the fluctuation theorem to nonequilibrium steady states at long time scales in the asymptotic limit. To this end, a theoretical and/or purely numerical model of the integral fluctuation theorem has been presented. An approximate general expression for the dissipation function has been derived for accelerated colloidal systems trapped/confined in power-law traps. Thereafter, a colloidal particle trapped in a harmonic potential (generated by an accelerating one-dimensional optical trap) and undergoing Brownian motion has been considered for the numerical study. A toy model of a quartic potential trap in addition to the harmonic trap has also been considered for the numerical study. The results presented herein show that the integral fluctuation theorem applies not only to equilibrium steady state distributions but also to nonequilibrium steady state distributions of colloidal systems in accelerated frames of reference over long time scales.

A Thermodynamic Model for Nearest-Neighbor Distributions in Annealed Quaternary Alloys

2011 ◽  
Vol 383-390 ◽  
pp. 768-773
Author(s):  
Li Li Tang ◽  
Chun Bo Wang
Keyword(s):  
Nearest Neighbor ◽  
Blue Shift ◽  
Type Conversion ◽  
Quaternary Alloys ◽  
Separation Result ◽  
Atomic Relaxation ◽  
Long Time ◽  
Higher Temperature ◽  
Induced Changes ◽  
Short Time

We focus on the annealing-induced changes of N-centered nearest-neighbor (NN) entironment in Ga1-xlnxNyAs1-y quaternary alloys and present a statistical distributing model of the binary bonds under thermodynamics equilibrium state. The core of this model is the assumption that the phase separation result of equimolar system at T=0 K is “ + ”, in which the effect of strain has been ignored. We propose two mechanisms for annealing: (i) Atomic relaxation lead to a total energy minimum. (ii) The type conversion of bond configuration is the main reason for the remarkable blue shift. Then parameter r, the number of NN In atoms per N atom, is calculated. We find that the theoretical NN distributions strain is in good agreement with former studies. It can be concluded that the blue shift induced by long-time annealing at low temperature is able to be equal with that induced by short-time annealing at higher temperature. The results are close to recent investigations. But an allegorical linear relation between band gap and composition (x, y) is still in question.

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