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131.
A drawback to using local search algorithms to address NP-hard discrete optimization problems is that many neighborhood functions have an exponential number of local optima that are not global optima (termed L-locals). A neighborhood function η is said to be stable if the number of L-locals is polynomial. A stable neighborhood function ensures that the number of L-locals does not grow too large as the instance size increases and results in improved performance for many local search algorithms. This paper studies the complexity of stable neighborhood functions for NP-hard discrete optimization problems by introducing neighborhood transformations. Neighborhood transformations between discrete optimization problems consist of a transformation of problem instances and a corresponding transformation of solutions that preserves the ordering imposed by the objective function values. In this paper, MAX Weighted Boolean SAT (MWBS), MAX Clause Weighted SAT (MCWS), and Zero-One Integer Programming (ZOIP) are shown to be NPO-complete with respect to neighborhood transformations. Therefore, if MWBS, MCWS, or ZOIP has a stable neighborhood function, then every problem in NPO has a stable neighborhood function. These results demonstrate the difficulty of finding effective neighborhood functions for NP-hard discrete optimization problems.This research is supported in part by the Air Force Office of Scientific Research (F49620-01-1-0007, FA9550-04-1-0110).  相似文献   
132.
Recent studies reveal that amorphous intermediates are involved in the formation of clathrate hydrates under conditions of high driving force, raising two questions: first, how could amorphous nuclei grow into crystalline clathrates and, second, whether amorphous nuclei are intermediates in the formation of clathrate crystals for temperatures close to equilibrium. In this work, we address these two questions through large-scale molecular simulations. We investigate the stability and growth of amorphous and crystalline clathrate nuclei and assess the thermodynamics and kinetic factors that affect the crystallization pathway of clathrates. Our calculations show that the dissociation temperature of amorphous clathrates is just 10% lower than for the crystals, facilitating the formation of metastable amorphous intermediates. We find that, at any temperatures, the critical crystalline nuclei are smaller than critical amorphous nuclei. The temperature dependence of the critical nucleus size is well described by the Gibbs-Thomson relation, from which we extract a liquid-crystal surface tension in excellent agreement with experiments. Our analysis suggests that at high driving force the amorphous nuclei may be kinetically favored over crystalline nuclei because of lower free energy barriers of formation. We investigated the role of the initial structure and size of the nucleus on the subsequent growth of the clathrates, and found that both amorphous and sI crystalline nuclei yield crystalline clathrates. Interestingly, growth of the metastable sII crystal polymorph is always favored over the most stable sI crystal, revealing kinetic control of the growth and indicating that a further step of ripening from sII to sI is needed to reach the stable crystal phase. The latter results are in agreement with the observed metastable formation of sII CO(2) and CH(4) clathrate hydrates and their slow conversion to sI under experimental conditions.  相似文献   
133.
Romano  Luigi  Timpone  Francesco  Bruzelius  Fredrik  Jacobson  Bengt 《Meccanica》2022,57(1):165-191
Meccanica - This paper establishes new analytical results in the mathematical theory of brush tyre models. In the first part, the exact problem which considers large camber angles is analysed from...  相似文献   
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The A2A adenosine receptor is a protein belonging to a family of four GPCR adenosine receptors. It is involved in the regulation of several pathophysiological conditions in both the central nervous system and periphery. In the brain, its localization at pre- and postsynaptic level in striatum, cortex, hippocampus and its effects on glutamate release, microglia and astrocyte activation account for a crucial role in neurodegenerative diseases, including Alzheimer’s disease (AD). This ailment is considered the main form of dementia and is expected to exponentially increase in coming years. The pathological tracts of AD include amyloid peptide-β extracellular accumulation and tau hyperphosphorylation, causing neuronal cell death, cognitive deficit, and memory loss. Interestingly, in vitro and in vivo studies have demonstrated that A2A adenosine receptor antagonists may counteract each of these clinical signs, representing an important new strategy to fight a disease for which unfortunately only symptomatic drugs are available. This review offers a brief overview of the biological effects mediated by A2A adenosine receptors in AD animal and human studies and reports the state of the art of A2A adenosine receptor antagonists currently in clinical trials. As an original approach, it focuses on the crucial role of pharmacokinetics and ability to pass the blood–brain barrier in the discovery of new agents for treating CNS disorders. Considering that A2A receptor antagonist istradefylline is already commercially available for Parkinson’s disease treatment, if the proof of concept of these ligands in AD is confirmed and reinforced, it will be easier to offer a new hope for AD patients.  相似文献   
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Citrus bioflavonoids are polyphenolic plant-derived pigments found in high levels in oranges, lemons, grapefruits and other citrus fruits. The three most abundant types of citrus bioflavonoids are hesperidin, naringenin and eriocitrin. Citrus bioflavonoids have long been known to possess powerful free radical-scavenging properties and cardioprotective effects. The study involved the analysis of 10 commercially available citrus bioflavonoid supplements from three different countries: Australia, the United States and Canada. The supplements were tested for their citrus bioflavonoid content which varied from 0.8 to 33.3% w/w. The daily bioflavonoid dose varied from 19 mg to 560 mg. Hesperidin was the major citrus bioflavonoid in nine out of ten supplements. One supplement was found to contain less than 10% of the quantity of rutin claimed to have been added. The DPP-4 inhibitory potential, compared through an estimation of rutin equivalence, ranged from 1.9 mg to 400 mg per day. This data highlights the variability between the supplements in their potential to inhibit DPP-4 for subsequent health benefits.  相似文献   
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The adenosine A3 receptor is a promising target for treating and diagnosing inflammation and cancer. In this paper, a series of bicyclo[3.1.0]hexane-based nucleosides was synthesized and evaluated for their P1 receptor affinities in radioligand binding studies. The study focused on modifications at 1-, 2-, and 6-positions of the purine ring and variations of the 5′-position at the bicyclo[3.1.0]hexane moiety, closing existing gaps in the structure–affinity relationships. The most potent derivative 30 displayed moderate A3AR affinity (Ki of 0.38 μM) and high A3R selectivity. A subset of compounds varied at 5′-position was further evaluated in functional P2Y1R assays, displaying no off-target activity.  相似文献   
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Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design.

Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood.  相似文献   
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