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This article explores electronic transport in a triple quantum dot system connected in parallel to metallic leads while subjected to an external magnetic flux. The Green-function formalism and the equation of motion approach were employed to derive a comprehensive formula for conductance. The study reveals the presence and modulation of Fano and Dicke effects in the conductance spectra of the Triple quantum dot system (TQD). These effects are controlled by adjusting the interdot coupling energy ( ), the coupling (Γ) of the three dots to the right and left leads, and manipulating the external magnetic flux.

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Relating a protein's sequence to its conformation is a central challenge for both structure prediction and sequence design. Statistical contact potentials, as well as their more descriptive versions that account for side‐chain orientation and other geometric descriptors, have served as simplistic but useful means of representing second‐order contributions in sequence–structure relationships. Here we ask what happens when a pairwise potential is conditioned on the fully defined geometry of interacting backbones fragments. We show that the resulting structure‐conditioned coupling energies more accurately reflect pair preferences as a function of structural contexts. These structure‐conditioned energies more reliably encode native sequence information and more highly correlate with experimentally determined coupling energies. Clustering a database of interaction motifs by structure results in ensembles of similar energies and clustering them by energy results in ensembles of similar structures. By comparing many pairs of interaction motifs and showing that structural similarity and energetic similarity go hand‐in‐hand, we provide a tangible link between modular sequence and structure elements. This link is applicable to structural modeling, and we show that scoring CASP models with structured‐conditioned energies results in substantially higher correlation with structural quality than scoring the same models with a contact potential. We conclude that structure‐conditioned coupling energies are a good way to model the impact of interaction geometry on second‐order sequence preferences. [ABSTRACT FROM AUTHOR]

Density functional theory investigation is performed to understand the underlying mechanism of hydrogen adsorption in the MOF-5 by using for first time the connector structure. The analysis of chemical bonds of the connector's atoms shows a good agreement between experimental and theoretical results. In particular, we show that this material has a desorption temperature of 115 K and an initial hydrogen storage capacity around 1.57 wt% which are close to the experimental values. We consider the coupling-energy mechanism to explore the most stable configurations in multiple adsorption sites namely metallic, carboxylic and cyclic sites. Three orientations which are vertical, horizontal and sloping are taking into account. The results show that the metallic and cyclic sites are more stable for multiple hydrogen molecule storage and the system reaches 4.57 wt% as a gravimetric storage capacity which is located in the interval 4.50–5.20 wt% found experimentally. In addition, the desorption temperature is improved significantly. Adsorption of several H 2 hydrogen molecules in the connector -MOF-5. Image 1 [ABSTRACT FROM AUTHOR]

The asymptotic homogenization of periodic network materials modeled as beam networks is pursued in this contribution, accounting for surface effects arising from the presence of a thin coating on the surface of the structural beam elements of the network. Cauchy and second gradient effective continua are considered and enhanced by the consideration of surface effects. The asymptotic homogenization technique is here extended to account for the additional surface properties, which emerge in the asymptotic expansion of the effective stress and hyperstress tensors versus the small scale parameters and the additional small parameters related to surface effects. Based on the elaboration of small dimensionless parameters of geometrical or mechanical nature reflecting the different length scales, we construct different models in which the importance of surface effects is dictated by specific choice of the scaling relations between the introduced small parameters. The effective moduli reflect the introduced surface properties. We show in particular that surface effects may become dominant for specific choices of the scaling laws of the introduced small parameters. Examples of networks are given for each class of the considered effective constitutive models to illustrate the proposed general framework. [ABSTRACT FROM AUTHOR]

Quantitative measurement of intramolecular and intermolecular interactions in protein structure is an elusive task, not easy to address experimentally. The phenomenon denoted ‘energetic coupling’ describes short- and long-range interactions between two residues in a protein system. A powerful method to identify and quantitatively characterize long-range interactions and allosteric networks in proteins or protein–ligand complexes is called double-mutant cycles analysis. In this review we describe the thermodynamic principles and basic equations that underlie the double mutant cycle methodology, its fields of application and latest employments, and caveats and pitfalls that the experimentalists must consider. In particular, we show how double mutant cycles can be a powerful tool to investigate allosteric mechanisms in protein binding reactions as well as elusive states in protein folding pathways.

A quantum mesoscopic electrical LC-circuit with charge discreteness including a Josephson junction is considered and a nonlinear Hamiltonian that describing the dynamic of such circuit is introduced. The quantum dynamical behavior (persistent current probability) is studied in the charge and phase regimes by numerical solution approaches. The time evolution of charge and current, number-difference and the bosonic phase and also the energy spectrum of a quantum mesoscopic electric LC-circuit with charge discreteness that coupled with a Josephson junction device are investigated. We show the role of the coupling energy and the electrostatic Coulomb energy of the Josephson junction in description of the quantum behavior and the spectral properties of a quantum mesoscopic electrical LC-circuits with charge discreteness. [ABSTRACT FROM AUTHOR]

The quantum theory for a mesoscopic electric circuit including a Josephson junction with charge discreteness is studied. By considering coupling energy of the mesoscopic capacitor in Josephson junction device, a Hamiltonian describing the dynamics of a quantum mesoscopic electric LC-circuit with charge discreteness is introduced. We first calculate the persistent current on a quantum driven ring including Josephson junction. Then we obtain the persistent current and energy spectrum of a quantum mesoscopic electrical circuit which includes capacitor, inductor, time-dependent external source and Josephson junction. [ABSTRACT FROM AUTHOR]

We designed and manufactured a novel annular-core hollow beam fiber which could directly yield ring light with a central dark spot inside the beam employing MCVD technique and a custom-made fiber drawing tower. The tapered fiber zone geometric shapes at varied stretching speed between the single-core fiber and the annular-core hollow beam fiber were studied theoretically. According to the beam propagation method, the bi-tapered coupling energy transmission between these two fibers was simulated and analyzed. Moreover, by adopting a fusion splicing and stretching technique at the fiber-linked point, an effective coupling approach had been fulfilled. [ABSTRACT FROM AUTHOR]

The inelastic electron tunneling spectroscopy (IETS) of bi-octane-monothiol junctions is theoretically studied based on first-principles calculations. The results reveal that IETS is very sensitive to the vertical and lateral distance of the two molecules in the bimolecular junctions owing to the changes of interaction between the two molecules. It is further demonstrated that the transverse vibrational modes ν(C-H) around 0.38 V will be triggered when the two molecules are close to each other and open a new path for electron tunneling. Our theoretical results provide new insight into understanding the origin of the IETS peaks around 0.38 V. [ABSTRACT FROM AUTHOR]

The cys-loop receptors are neurotransmitter-operated ion channels, which mediate fast synaptic transmission for communication between neurons. However, prolonged exposure to the neurotransmitter drives the receptor to a desensitization state, which plays an important role in shaping synaptic transmission. Much progress has been made through more than half a century's research since Katz and Thesleff first descried desensitization for muscle nicotinic acetylcholine receptor. In this review, we summarized recent research developments of receptor desensitization. Now, it has been identified that many parts of the receptor, such as the pore domain (including the hinge in the M2-M3 linker), the binding domain, the coupling region, and the intracellular domain, are all involved in the cys-loop receptor desensitization and that uncoupling between the amino-terminal domain and channel lining domain seems to play a central role in desensitization. This uncoupling is mainly governed by the balance between coupling strength and relative tightness of gating machinery and influenced by other parts of the receptor. Agonist binding induces conformational change to overcome the gating barrier to open the channel through the stressed coupling region, which is subsequently broken, causing receptor desensitization. With rapid advancement in structural biology of membrane receptors, final validation of this mechanism is expected to occur in the near future when the high-resolution structure of the desensitized state is available. [ABSTRACT FROM AUTHOR]

The energetic networks that govern regulated switching processes in macromolecules are poorly understood at a molecular level. We illustrate a general methodology that uses thermodynamic cycles to measure the coupling energetics between specific groups in a macromolecule and ligand-binding-induced macromolecular switching. The approach is applied to new and published thermodynamic stability and/or binding data not previously analyzed in this way, for a wide range of switching systems, including H+ or Ca2+-binding-induced myristoyl switching, ion or peptide-binding-induced conformational switching in various proteins and small molecule binding to a ribo-switch. The results show how this powerful approach can be used to identify and dissect the molecular determinants of switching in macromolecules. [ABSTRACT FROM AUTHOR]

We present a new theoretical approach to determine the interaction energy due to the coupling of adsorbed molecules to their environment in scanning tunneling microscopy. In fact, the above coupling energy is estimated by assuming the involved adsorbed molecules as Morse oscillators and their environment (electrodes, leads) as external reservoir. [ABSTRACT FROM AUTHOR]

Abstract: Our previous study has suggested that mutation of the amino acid residue Asp102 has a significant effect on the fumarate-mediated activation of human mitochondrial NAD(P)+-dependent malic enzyme (m-NAD(P)-ME). In this paper, we examine the cationic amino acid residue Arg98, which is adjacent to Asp102 and is highly conserved in most m-NAD(P)-MEs. A series of R98/D102 mutants were created to examine the possible interactions between Arg98 and Asp102 using the double-mutant cycle analysis. Kinetic analysis revealed that the catalytic efficiency of the enzyme was severely affected by mutating both Arg98 and Asp102 residues. However, the binding energy of these mutant enzymes to fumarate as determined by analysis of the K A,Fum values, show insignificant differences, indicating that the mutation of Arg98 and Asp102 did not cause a significant decrease in the binding affinity of fumarate. The overall coupling energies for R98K/D102N as determined by analysis of the k cat/K m and K A,Fum values were −2.95 and −0.32kcal/mol, respectively. According to these results, we conclude that substitution of both Arg98 and Asp102 residues has a synergistic effect on the catalytic ability of the enzyme. [Copyright &y& Elsevier]

Understanding the molecular principles that govern allosteric communication is an important goal in protein science. One way allostery could be transmitted is via sparse energetic networks of residues, and one such evolutionary conserved network was identified in the PDZ domain family of proteins by multiple sequence alignment [Lockless SW, Ranganathan R (1999) Science 286:295-299]. We have reassessed the energetic coupling of these residues by double mutant cycles together with ligand binding and stability experiments and found that coupling is not a special property of the coevolved network of residues in PDZ domains. The observed coupling for ligand binding is better explained by a distance relationship, where residues close in space are more likely to couple than distal residues. Our study demonstrates that statistical coupling from sequence analysis is not necessarily a reporter of energetic coupling and allostery. [ABSTRACT FROM AUTHOR]

Abstract: Bipolaron states in a quasi-0D quantum dot with a spherical parabolic confinement potential are investigated by applying the Feynman variational principle. The bipolaron coupling energy and self-action potential energy are found to increase with an increase in the Fröhlich electron–phonon-coupling constant. There is also a non-monotonic dependence of the bipolaron coupling energy on the quantum dot radius. With decreasing structure radius the bipolaron coupling energy increases. However, from a critical radius it starts decreasing as the radius decreases, due to the dominance of the coulomb-to-phonon mediated interaction. When electrons in the bipolaron are forcefully neighboured, the polarization of the structure is intensified and consequently there is Coulomb repulsion. The possibility of bipolaron formation depends on the strength of the direct Coulomb repulsion which, in turn, depends on the quantum dot radius. The main contribution to the bipolaron coupling energy comes from the self-action potential. This self-action potential energy influences the energy state of the bipolaron considerably. The ratio of optical-to-static dielectric constants significantly affects the bipolaron coupling energy. [Copyright &y& Elsevier]

Binding of neurotransmitter triggers gating of synaptic receptor channels, but our understanding of the structures that link the binding site to the channel is just beginning to develop. Here, we identify an intersubunit triggering element required for rapid and efficient gating of muscle nicotinic receptors using a structural model of the Torpedo receptor at 4 Å resolution, recordings of currents through single receptor channels, measurements of inter-residue energetic coupling, and functional consequences of disulfide trapping. Mutation of the conserved residues, αTyr 127, εAsn 39, and δAsn 41, located at the two subunit interfaces that form the agonist binding sites, markedly attenuates acetylcholine-elicited channel gating; mutant cycle analyses based on changes in the channel gating equilibrium constant reveal strong energetic coupling among these residues. After each residue is substituted with Cys, oxidizing conditions that promote disulfide bond formation attenuate gating of mutant, but not wild-type receptors. Gating is similarly attenuated when the Cys substitutions are confined to either of the binding-site interfaces, but can be restored by reducing conditions that promote disulfide bond breakage. Thus, the Tyr-Asn pair is an intersubunit trigger of rapid and efficient gating of muscle nicotinic receptors. [ABSTRACT FROM AUTHOR]

Abstract: We have investigated the functional network of hotspot residues at the remote docking site of two cell cycle regulators, namely Cdc25B phosphatase and its native protein substrate Cdk2-pTpY/CycA. Specifically, we have studied the roles of energetically important residues (Arg488, Arg492, Tyr497 on Cdc25B and Asp206 and Asp210 on Cdk2-pTpY/CycA) by generating a diverse set of substitutions and performing double and triple mutant cycle analyses. This transient protein–protein interaction is particularly well-suited for this mutagenic approach because various control experiments ensure that the effect of each mutation is limited to the interaction of interest. We find binary coupling energies for ion pairs and hydrogen bonds ranging from 0.7 kcal/mol to 3.9 kcal/mol and ternary coupling energies of 1.9 kcal/mol and 2.8 kcal/mol. Overall our biochemical analyses are in good agreement with the docked structure of the complex and suggest the following roles for the individual hotspot residues on Cdc25B. The most important contributor, Arg492, forms a specific and tight bidentate interaction with Asp206 and a weaker interaction with Asp210 that cannot be replaced by a Lys. Although Tyr497 does not directly participate in this ionic network, it is important for buttressing Arg492 using both its hydrophobic (aromatic ring) and hydrophilic characteristics (hydrogen bonding). Arg488 participates less specifically in the electrostatic network with Asp206 and Asp210 of the protein substrate as it can partially be replaced by Lys. Our data provide insight how a cluster of residues in a docking site remote from the site of the chemical reaction can bring about efficient and specific substrate recognition. [Copyright &y& Elsevier]

Abstract: In this paper we study the magnetoresistance and the coupling energy in heterostructures formed by two magnetic layers Ga1− x Mn x As separated by a nonmagnetic spacer GaAs under an electric field and develop a mean-field theory of carrier in diluted magnetic semiconductor. Our main result indicates that magnetoresistance can be dramatically suppressed by an external electric field. [Copyright &y& Elsevier]

Abstract: Spin injection in low-dimensional semiconductors have a great potential to be used in magnetoelectronics and spintronics. In our work we analyze the electronic properties of the hole gas formed in Ga1-xMnxAs/GaAs/Ga1-xMnxAs heterostructures. We find that there is an RKKY-type exchange coupling between the magnetic layers that oscillates between ferromagnetic and antiferromagnetic as a function of the different parameters of the problem. As an example we calculate the spin-dependent hole density, the polarization and the coupling energy, using an efficient self-consistent procedure to solve simultaneously the Schrödinger and Poisson equations, taking into account the interaction with Mn magnetic moments. Our results indicate that the coupling energy also oscillates in terms of the band offset Vw which describes the difference in electronegativity between the Mn and GaAs atoms. [Copyright &y& Elsevier]

This paper studied the time evolution of quantum state in a mesoscopic LC circuit with the coupling energy caused by mesoscopic capacitor acting as a tunnel junction. It indicates that the state of the junction evolves into the quantum superposition of two coherent states and, in the state, nonclassical squeezing properties of the circuit appear. It also indicates that the dynamic behavior of the current shows collapse and revival phenomenon. The research in the paper will be helpful to miniaturize integrate circuits and electric components. It will be also important for the utilization of mesoscopic circuits to evolve the quantum states, which work as information carriers. [ABSTRACT FROM AUTHOR]

We have fabricated a vertical quantum dot with lateral coupling, modulated by a split gate voltage, to a two-dimensional electron. We thereby control not only electron configurations but also the strength of coupling between the dot and the lateral lead, by applying gate voltages. We have measured the conductance enhancement when the applied bias exceeds the single-electron excitation energy, in the Coulomb blockade regime. This conductance enhancement disappears as the split gate voltage decreases (reducing the coupling). This indicates that this enhancement is caused by inelastic co-tunneling. Furthermore, we observed a conductance enhancement at zero source–drain bias with stronger coupling. An anomaly is observed that we attribute to Kondo resonance between the dot and the leads. [Copyright &y& Elsevier]

Relating a protein's sequence to its conformation is a central challenge for both structure prediction and sequence design. Statistical contact potentials, as well as their more descriptive versions that account for side-chain orientation and other geometric descriptors, have served as simplistic but useful means of representing second-order contributions in sequence-structure relationships. Here we ask what happens when a pairwise potential is conditioned on the fully defined geometry of interacting backbones fragments. We show that the resulting structure-conditioned coupling energies more accurately reflect pair preferences as a function of structural contexts. These structure-conditioned energies more reliably encode native sequence information and more highly correlate with experimentally determined coupling energies. Clustering a database of interaction motifs by structure results in ensembles of similar energies and clustering them by energy results in ensembles of similar structures. By comparing many pairs of interaction motifs and showing that structural similarity and energetic similarity go hand-in-hand, we provide a tangible link between modular sequence and structure elements. This link is applicable to structural modeling, and we show that scoring CASP models with structured-conditioned energies results in substantially higher correlation with structural quality than scoring the same models with a contact potential. We conclude that structure-conditioned coupling energies are a good way to model the impact of interaction geometry on second-order sequence preferences., (© 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

Transfer efficiencies between phycobilisomes and photosystem II antenna chlorophylls were determined on membrane fragments isolated from low and high light adapted Anabaena cells. The observed increase in energy transfer in high light adapted cells is a consequence of shorter interchromophore distances and a decrease in the number of jumps of the exciting photons. Calculation of the rates of energy transfer and the coupling energies indicate that the weak interaction inferred for energy transfer between phycobilisome and photosystem II in low light adapted cells is replaced by an intermediate interaction in high light adapted cells. [ABSTRACT FROM AUTHOR]

Quantitative measurement of intramolecular and intermolecular interactions in protein structure is an elusive task, not easy to address experimentally. The phenomenon denoted 'energetic coupling' describes short- and long-range interactions between two residues in a protein system. A powerful method to identify and quantitatively characterize long-range interactions and allosteric networks in proteins or protein-ligand complexes is called double-mutant cycles analysis. In this review we describe the thermodynamic principles and basic equations that underlie the double mutant cycle methodology, its fields of application and latest employments, and caveats and pitfalls that the experimentalists must consider. In particular, we show how double mutant cycles can be a powerful tool to investigate allosteric mechanisms in protein binding reactions as well as elusive states in protein folding pathways.