Ab initio investigation of the I-V characteristics of the butadiene nano-molecular wires: A light-driven molecular switch

We apply a first-principles computational approach to study a light-sensitive molecular switch. The molecule that comprises the switch can convert between a trans and a cis configuration upon photoexcitation. We find that the conductance of the two isomers varies dramatically, which suggests that this system has potential application as a molecular device. A detailed analysis of the projection of the density of states (PDOS) and the transmission coefficients T(E) of the system reveals the mechanism of the switch.     

1,3-diphenyltriazene as a possible optical molecular switch: A first-principles study

By applying nonequilibrium Green's function formalism combined with first-principles density functional theory, we investigate the electronic transport properties of a 1,3-diphenyltriazene-based optical molecular switch. The molecule that comprises the switch can convert between the cis and the trans forms upon photoexcitation. The transmission spectra of two forms are remarkably distinctive. Theoretical results show that the current through the trans form is significantly larger than that through the cis form, which suggests that this system has attractive potential application in future molecular switch technology.     

Phenylazoimidazole as a possible optical molecular switch: An ab initio study

By applying nonequilibrium Green's function formalism combined first-principles density functional theory, we investigate the electronic transport properties of the phenylazoimidazole optical molecular switch. The molecule that comprises the switch can convert between the cis and the trans forms upon photoexcitation. The influence of HOMO–LUMO gaps and the spatial distributions of molecular orbitals on the electronic transport through the molecular device are discussed in detail. Theoretical results show that the current through the trans form is significantly larger than through the cis form, which suggests this system has attractive potential application in future molecular switch technology.     

Theoretical investigation of the O2 adsorption effect in the electron transport of single Fe-porphyrin molecule

The effect of O₂ adsorption on the electron transport behavior of Fe-porphyrin molecule is investigated by the first-principles computational approach. The current-voltage characteristics of Fe-porphyrin and O₂ adsorbed Fe-porphyrin between gold electrodes are calculated. We find that the conductance of the Fe-porphyrin decreases dramatically upon the adsorption of O₂, which suggests that this system has potential application as a molecular sensor or a switch. This switching-behavior is analyzed from the evolutions of the transmission spectra and the molecular projected self-consistent Hamiltonian states of the molecular systems.     

First-principles study of the electronic transport properties of the anthraquinone-based molecular switch

By applying non-equilibrium Green’s function (NEGF) formalism combined with first-principles density functional theory (DFT), we have investigated the electronic transport properties of the anthraquinone-based molecular switch. The molecule that comprises the switch can be converted between the hydroquinone (HQ) and anthraquinone (AQ) forms via redox reactions. The transmission spectra of these two forms are remarkably distinctive. Our results show that the current through the HQ form is significantly larger than that through the AQ form, which suggests that this system has attractive potential application in future molecular switch technology.     

A terahertz molecular switch

We present time-dependent results describing the current through a molecular device, modeled as a complex with two active centers connected to leads under bias. We show that, at a properly adjusted external voltage, a passing terahertz electromagnetic pulse may cause a transition between states of finite and negligible current, suggesting that the system might be useful as a nanoscopic switch in the terahertz range. A phase diagram defining the bias region in which the transition takes place within a short time is given. As described, the physical processes involved are of an entirely different nature than those in ordinary photodetectors.     

Electronic transport properties of a diarylethene-based molecular switch with single-walled carbon nanotube electrodes: The effect of chirality

We have studied the electronic transport properties of an optical molecular switch based on the diarylethene molecule with two single-walled carbon nanotube (SWCNT) electrodes using first-principles transport calculations. It is shown that the closed form shows an overall higher conductance than the open form at low bias which is independent of the SWCNTs’ chirality. Meanwhile, the conductance of the molecular switch can be tuned by changing the chirality of the SWCNTs.     

First-principles study of the switching characteristics of the 15,16-dinitrile DDP/CPD-based optical molecular switch with carbon nanotube electrodes

We have studied the switching characteristics of an optical molecular switch based on the 15,16-dinitrile dihydropyrene/cyclophanediene (DDP/CPD) molecule with two single-walled carbon nanotube (SWCNT) electrodes using first-principles transport calculations. It is shown that the DDP shows an overall higher conductance than the CPD at low bias which is independently of the SWCNT chirality. Meantime, the conductance of the molecular switch can be tuned by the chirality of the SWCNT.     

Two-step enantio-selective optical switch

We present an optical "enantio-selective switch" that, in two steps, turns a ("racemic") mixture of left-handed and right-handed chiral molecules into the enantiomerically pure state of interest. The optical switch is composed of an "enantio-discriminator" and an "enantio-converter" acting in tandem. The method is robust, insensitive to decay processes, and does not require molecular preorientation. We demonstrate the method on the purification of a racemate of (transiently chiral) D2S2 molecules, performed on the nanosecond time scale.     

Carbon nanotubes as substrates for molecular spiropyran-based switches

We present a joint theory-experiment study investigating the excitonic absorption of spiropyran-functionalized carbon nanotubes. The functionalization is promising for engineering switches on a molecular level, since spiropyrans can be reversibly switched between two different conformations, inducing a distinguishable and measurable change of optical transition energies in the substrate nanotube. Here, we address the question of whether an optical read-out of such a molecular switch is possible. Combining density matrix and density functional theory, we first calculate the excitonic absorption of pristine and functionalized nanotubes. Depending on the switching state of the attached molecule, we observe a red-shift of transition energies by about 15?meV due to the coupling of excitons with the molecular dipole moment. Then we perform experiments measuring the absorption spectrum of functionalized carbon nanotubes for both conformations of the spiropyran molecule. We find good qualitative agreement between the theoretically predicted and experimentally measured red-shift, confirming the possibility for an optical read-out of the nanotube-based molecular switch.     

First-principles study of phenyl ethylene oligomers as current-switch

We use a self-consistent method to study the distinct current-switch of 2′-amino-4-ethynylphenyl-4′-ethynylphenyl-5′-nitro-1-benzenethiol, from the first-principles calculations. The switch behavior is in accord with the early experiment [M.A. Reed, J.H. Tour, Sci. Am. 282 (2000) 86]. To further investigate the transport mechanism of the conformational molecular switch, we calculate the switching behavior of p-terphenyl with the rotations of the middle ring as well, the results are consistent with Reed's experiment. We also study the effect of the hydrogen atom substituting one ending sulfur atom on the transport and find that the asymmetry of I–V curves appears and the switch effect still lies in both the positive and negative bias range.     

库仑位垒附近熔合反应的研究

利用改进的量子分子动力学研究了16?O?+?16?O库仑位垒附近的熔合反应,用连接函数的方法对体系的表面能做了改进.利用这种方法避免了非物理的核子发射,熔合截面有了明显的增加,这是因为体系的表面形变效应可以通过连接函数来体现,从而抑制了弹靶在熔合过程中非物理的核子发射.     

Effects of input noise on a simple biochemical switch

Many biological processes are controlled by biomolecular switches which themselves are regulated by various upstream chemical molecules (the input). Understanding how input noise affects the output stochastic switching process is of significant interest in various biophysical systems like gene regulation, chemosensing, and cell motility. Here, we propose an exactly solvable model where the noisy input signal arises from a simple birth-death process and directly regulates the transition rates of a downstream switch. We solve the joint master equations to analyze the statistical properties of the output switching process. Our results suggest that the conventional wisdom of an additive input-output noise rule fails to describe signaling systems containing a single molecular switch, and, instead, the most important effect of input noise is to effectively reduce the on rate of the switch.     

A possible salicylideneanilines-based optical molecular switch induced by a reversible hydrogen transfer: an ab initio study

The electronic transport properties of the salicylideneanilines-based molecular optical switch are investigated using a nonequilibrium Green's function formalism combined with first-principles density functional theory. The molecule that comprises the switch can convert between the enol and keto tautomeric forms upon photoinduced excited state hydrogen transfer in the molecular bridge. Theoretical results show that the current through the enol form is significantly larger than that through the keto form, which realize the on and off states of the molecular switch. The physical origin of the switching behaviour is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap. Furthermore the effect of the donor/acceptor substituent on the electronic transport through the molecular device is also discussed in detail. The switching performance can be improved to some extent through the acceptor substituent.     

Study of spatial signal transduction in bistable switches

Bistable switch modules are among the most important fundamental motifs in signal-transduction pathways. To better understand their spatial signal transduction, we model the diffusion process in the one-dimensional (1–D) domain. We find that when none of the elements diffuse, the response of the system exhibits a spatial switch–like property. However, when one of the elements is highly diffusible, the response of the system does not show any spatial switching behavior. Furthermore, we observe that the spatial responses of the system are more sensitive to the time constant of the switch when none of the elements are diffusible. Further, a slow loop keeps the system in the high steady state more positions than that in the fast loop. Finally, we consolidate our numerical results analytically by performing a mathematical method.     

Quantum Phase Transition and Thermal Entanglement in the Isotropic XXX Model

We investigate the quantum phase transition (QPT) and the pairwise thermal entanglement in the three-qubit Heisenberg XXX chain with Dzyaloshinskii--Moriya (DM) interaction under a magnetic field. The ground states of the system exist crossing points, which shows that the system exhibits a QPT. At a given temperature, the entanglement undergoes two sudden changes (platform-like behavior) as the DM interaction or external magnetic field increases. This special property can be used as the entanglement switch, which is also influenced by the temperature. We can modulate the DM interaction or external magnetic field to control the entanglement switch.     

Heat switch effect in one-dimensional spin chains

We study heat transport in one-dimensional (1-D) quantum spin systems by the nonequilibrium Green?s function method. We show that, in both ferromagnetic and antiferromagnetic systems, the excitation spectrums of the reservoirs and the central spin chain can be tuned to be matched or mismatched by changing the external magnetic field. When the spectrums are matched, heat current through the system is large; however if the spectrums are mismatched, heat current becomes much smaller. Through tuning the magnetic field, the system can thus act as a heat switch, and we discuss the condition for the system to exhibit strong switch effect.     

Controlling the charge state of a single redox molecular switch

Scanning tunneling microscopy and dynamic force microscopy in the noncontact mode are used in combination to investigate the reversible switching between two stable states of a copper complex adsorbed on a NaCl bilayer grown on Cu(111). The molecular conformation in these two states is deduced from scanning tunneling microscopy imaging, while their charge is characterized by the direct measurement of the tip-molecule electrostatic force. These measurements demonstrate that the molecular bistability is achieved through a charge-induced rearrangement of the coordination sphere of the metal complex, qualifying this system as a new electromechanical single-molecular switch.     

Protein-based molecular contrast optical coherence tomography with phytochrome as the contrast agent

We report the use of phytochrome A (phyA), a plant protein that can reversibly switch between two states with different absorption maxima (at 660 and 730 nm), as a contrast agent for molecular contrast optical coherence tomography (MCOCT). Our MCOCT scheme builds up a difference image revealing the distribution of phyA within a target sample from pairs of consecutive OCT A-scans acquired at a probe wavelength of 750 nm, both with and without additional illumination of the target sample with 660-nm light. We demonstrate molecular imaging with this new MCOCT modality in a target sample containing a mixture of 0.2% Intralipid and 83 microM of phyA.     

Computational study of the mechanism of Bcl-2 apoptotic switch

In spite of attention devoted to molecular mechanisms of apoptosis, the details of functioning of one crucial component–the Bcl-2 apoptotic switch–are not completely understood. There are two competing mechanisms of its internal working—the indirect activation and the direct activation. In the absence of conclusive experimental data, we have used computational modeling to assess the properties of both mechanisms and their suitability to act as a biological switch. Since the two mechanisms form opposite poles of continuum of Bcl-2 molecular interaction models, we have constructed more general models including these two models as extreme cases. By studying the relationship between model parameters and the steady-state response we have found optimal interaction patterns which reproduce the behavior of the Bcl-2 apoptotic switch. Our results show, that stimulus–response ultrasensitivity is negatively affected by spontaneous activation of Bcl-2 effectors. We found that ultrasensitivity requires effectors activation, mediated by another subgroup of Bcl-2 proteins—activators. We have shown that the auto-activation of monomeric effector forms provides an ultrasensitivity enhancing feedback loop. Thorough robustness analysis revealed that the interaction pattern postulated in the direct activation hypothesis is able to conserve stimulus–response switching characteristics for wide range changes of its internal parameters. The robustness of the switch against the variation of the reaction parameter is strongly reduced for the intermediate hybrid model and even more for the indirect part of the models. Computer simulations of the more general model presented here suggest, that stimulus–response ultrasensitivity is an emergent property of the direct activation model that is unlikely to occur in the model of indirect activation. Introduction of indirect-model-specific interactions does not provide a better explanation of the Bcl-2 switch functionality compared to the direct model.