Principle of local energy minimum for donor-acceptor systems with low compensation

1997 ◽  
Vol 111 (3) ◽  
pp. 754-761 ◽  
Author(s):  
V. N. Likhachev ◽  
V. A. Onischuk
Keyword(s):  
Local Energy ◽  
Energy Minimum ◽  
Local Energy Minimum ◽  
Donor Acceptor

p-WAVE PAIRING IN FERMI SYSTEMS WITH UNEQUAL POPULATION NEAR FESHBACH RESONANCE

2008 ◽  
Vol 22 (25n26) ◽  
pp. 4358-4366 ◽  
Author(s):  
KHANDKER F. QUADER ◽  
RENYUAN LIAO ◽  
FLORENTIN POPESCU
Keyword(s):  
Feshbach Resonance ◽  
Single Channel ◽  
Numerical Study ◽  
Fermi System ◽  
P Wave ◽  
Ground State Structure ◽  
Energy Minimum ◽  
Local Energy Minimum ◽  
Wave Pairing ◽  
Global Energy Minimum

We explore p-wave pairing in a single-channel two-component Fermi system with unequal population near Feshbach resonance. Our analytical and numerical study reveal a rich superfluid (SF) ground state structure as a function of imbalance. In addition to the state Δ±1 ∝ Y1±1, a multitude of “mixed” SF states formed of linear combinations of Y1m's give global energy minimum under a phase stability condition; these states exhibit variation in energy with the relative phase between the constituent gap amplitudes. States with local energy minimum are also obtained. We provide a geometric representation of the states. A T = 0 polarization vs. p-wave coupling phase diagram is constructed across the BEC-BCS regimes. With increased polarization, the global minimum SF state may undergo a quantum phase transition to the local minimum SF state.

scholarly journals Binding of HasA by its transmembrane receptor HasR follows a conformational funnel mechanism

2019 ◽  
Vol 49 (1) ◽  
pp. 39-57
Author(s):  
Thomas E. Exner ◽  
Stefanie Becker ◽  
Simon Becker ◽  
Audrey Boniface-Guiraud ◽  
Philippe Delepelaire ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Specific Binding ◽  
Md Simulations ◽  
Energy Minimum ◽  
Wild Type ◽  
Double Mutation ◽  
Starting Position ◽  
Local Energy Minimum ◽  
Type Complex ◽  
Heme Transfer

AbstractHasR in the outer membrane of Serratia marcescens binds secreted, heme-loaded HasA and translocates the heme to the periplasm to satisfy the cell’s demand for iron. The previously published crystal structure of the wild-type complex showed HasA in a very specific binding arrangement with HasR, apt to relax the grasp on the heme and assure its directed transfer to the HasR-binding site. Here, we present a new crystal structure of the heme-loaded HasA arranged with a mutant of HasR, called double mutant (DM) in the following that seemed to mimic a precursor stage of the abovementioned final arrangement before heme transfer. To test this, we performed first molecular dynamics (MD) simulations starting at the crystal structure of the complex of HasA with the DM mutant and then targeted MD simulations of the entire binding process beginning with heme-loaded HasA in solution. When the simulation starts with the former complex, the two proteins in most simulations do not dissociate. When the mutations are reverted to the wild-type sequence, dissociation and development toward the wild-type complex occur in most simulations. This indicates that the mutations create or enhance a local energy minimum. In the targeted MD simulations, the first protein contacts depend upon the chosen starting position of HasA in solution. Subsequently, heme-loaded HasA slides on the external surface of HasR on paths that converge toward the specific arrangement apt for heme transfer. The targeted simulations end when HasR starts to relax the grasp on the heme, the subsequent events being in a time regime inaccessible to the available computing power. Interestingly, none of the ten independent simulation paths visits exactly the arrangement of HasA with HasR seen in the crystal structure of the mutant. Two factors which do not exclude each other could explain these observations: the double mutation creates a non-physiologic potential energy minimum between the two proteins and /or the target potential in the simulation pushes the system along paths deviating from the low-energy paths of the native binding processes. Our results support the former view, but do not exclude the latter possibility.

Low-temperature enantiotropic k2 phase transition in the ionic 222-cryptand complex with LiClO4

2007 ◽  
Vol 63 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Ilia A. Guzei ◽  
Lara C. Spencer ◽  
Joe W. Su ◽  
Ronald R. Burnette
Keyword(s):  
Phase Transition ◽  
Gas Phase ◽  
Complex I ◽  
Global Minimum ◽  
Energy Minimum ◽  
Ordered Structure ◽  
Compound I ◽  
Positional Disorder ◽  
Local Energy Minimum ◽  
Disordered Structure

Crystallographic analyses at 100 and 200 K are reported for the macrobicyclic polyether 4,7,13,16,21,24-hexaoxa-1,10-diaza-bicyclo[8.8.8]hexacosane (denoted as 222-cryptand) that encapsulates a Li+ cation and then forms a complex (I) with ClO_4^-. Compound (I) undergoes a reversible second-order k phase transition at 253 (2) K from an almost ordered structure [space group P212121] at 100 K to a more disordered structure that exhibits a different unit cell [P21212 (2c′ = c)] above 253 (2) K. At 295 K the Li+ cation and five atoms of the perchlorate anion are each disordered over at least two positions about a crystallographic twofold axis [Chekhlov (2003). Russ. J. Coord. Chem. 29, 828–832]; as the temperature decreases the dynamic positional disorder is slowly frozen out, but is still observed for lithium even at 100 K. Based upon DFT computations, it seems that in the solid state the position of the Li+ cation in the cavity of the 222-cryptand below 253 (2) K likely corresponds to a local energy minimum; the global minimum in the gas phase corresponds to a near D 3 symmetrical conformation of the 222-cryptand with the undersized Li+ cation residing in the center of its cavity.

scholarly journals Exploring the Binding Mechanism and Dynamics of EndoMS/NucS to Mismatched dsDNA

2019 ◽  
Vol 20 (20) ◽  
pp. 5142
Author(s):  
Yanjun Zhang ◽  
Shengyou Huang
Keyword(s):  
Mismatch Repair ◽  
Md Simulations ◽  
Repair Process ◽  
Energy Curve ◽  
Energy Minimum ◽  
Recognition Mechanism ◽  
Local Energy Minimum ◽  
Closed State ◽  
Global Energy Minimum ◽  
Terminal Domains

The well-known mismatch repair (MMR) machinery, MutS/MutL, is absent in numerous Archaea and some Bacteria. Recent studies have shown that EndoMS/NucS has the ability to cleave double-stranded DNA (dsDNA) containing a mismatched base pair, which suggests a novel mismatch repair process. However, the recognition mechanism and the binding process of EndoMS/NucS in the MMR pathway remain unclear. In this study, we investigate the binding dynamics of EndoMS/NucS to mismatched dsDNA and its energy as a function of the angle between the two C-terminal domains of EndoMS/NucS, through molecular docking and extensive molecular dynamics (MD) simulations. It is found that there exists a half-open transition state corresponding to an energy barrier (at an activation angle of approximately 80 ∘ ) between the open state and the closed state, according to the energy curve. When the angle is larger than the activation angle, the C-terminal domains can move freely and tend to change to the open state (local energy minimum). Otherwise, the C-terminal domains will interact with the mismatched dsDNA directly and converge to the closed state at the global energy minimum. As such, this two-state system enables the exposed N-terminal domains of EndoMS/NucS to recognize mismatched dsDNA during the open state and then stabilize the binding of the C-terminal domains of EndoMS/NucS to the mismatched dsDNA during the closed state. We also investigate how the EndoMS/NucS recognizes and binds to mismatched dsDNA, as well as the effects of K + ions. The results provide insights into the recognition and binding mechanisms of EndoMS/NucS to mismatched dsDNA in the MMR pathway.

Evidence of a donor-acceptor type transition in CuGaSe2

1980 ◽  
Vol 41 (7) ◽  
pp. 707-712 ◽  
Author(s):  
A. Poure ◽  
G. Aguero ◽  
G. Masse ◽  
J.P. Aicardi
Keyword(s):  
Type Transition ◽  
Donor Acceptor

Photoactive donor-acceptor thin films as prospective materials for evaporated bulk heterojunctions of molecular semiconductors

2008 ◽  
Author(s):  
Derck Schlettwein ◽  
Robin Knecht ◽  
Dominik Klaus ◽  
Christopher Keil ◽  
Günter Schnurpfeil
Keyword(s):  
Thin Films ◽  
Bulk Heterojunctions ◽  
Donor Acceptor ◽  
Molecular Semiconductors
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