We use a novel optimization procedure that includes the temporal and spatial parameters of the pulses acting on arrays of trapped neutral atoms to prepare entangling gates in N-qubit systems. The ...spatiotemporal control allows treating a denser array of atoms, where each pulse acts on a subset of the qubits, potentially allowing to speed up the gate operation by two orders of magnitude by boosting the dipole-blockade between the Rydberg states. Studying the rate of success of the algorithm under different constraints, we evaluate the impact of the proximity of the atoms and, indirectly, the role of the geometry of the arrays in three and four-qubit systems, as well as the minimal energy requirements and how this energy is used among the different qubits. Finally, we characterize and classify all optimal protocols according to the mechanism of the gate using a quantum pathway analysis.
We predict anti-alignment dynamics in the excited state of H
2
+
or related homonuclear dimers in the presence of a strong field. This effect is a general indirect outcome of the strong transition ...dipole and large polarizabilities typically used to control or to induce alignment in the ground state. In the excited state, however, the polarizabilities have the opposite sign compared to those in the ground state, generating a torque that aligns the molecule perpendicular to the field, deeming any laser-control strategy impossible.
We predict anti-alignment dynamics in the excited state of H
2
+
or related homonuclear dimers in the presence of a strong field.
We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the spontaneous formation of nativelike ...structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A. An implicit solvent model combined with high-temperature MD makes it possible to perform direct folding simulations of small- to medium-sized proteins by reducing the computational requirements tremendously. In the early stage of folding of the villin headpiece and protein A, initial hydrophobic collapse and rapid formation of helices were found to play important roles. For protein A, the third helix forms first in the early stage of folding and exhibits higher stability. The free energy profiles calculated from the folding simulations suggested that both of the helix-bundle proteins show a two-state thermodynamic behavior and protein A exhibits rather broad native basins.
Activation entropy (ΔS ‡) is not normally considered the main factor in determining the reactivity of unimolecular reactions. Here, we report that the intramolecular degradation of six-membered ring ...compounds is mainly determined by the ΔS ‡, which is strongly influenced by the ring-flipping motion and substituent geometry. Starting from the unique difference between the pH-dependent degradation kinetics of geometric isomers of 1,2-cyclohexanecarboxylic acid amide (1,2-CHCAA), where only the cis isomer can readily degrade under weakly acidic conditions (pH < 5.5), we found that the difference originated from the large difference in ΔS ‡ of 16.02 cal·mol–1·K–1. While cis-1,2-CHCAA maintains a preference for the classical chair cyclohexane conformation, trans-1,2-CHCAA shows dynamic interconversion between the chair and twisted boat conformations, which was supported by both MD simulations and VT-NMR analysis. Steric repulsion between the bulky 1,2-substituents of the trans isomer is one of the main reasons for the reduced energy barrier between ring conformations that facilitates dynamic ring inversion motions. Consequently, the more dynamic trans isomer exhibits much a larger loss in entropy during the activation process due to the prepositioning of the reactant than the cis isomer, and the pH-dependent degradation of the trans isomer is effectively suppressed. When the ring inversion motion is inhibited by an additional methyl substituent on the cyclohexane ring, the pH degradability can be dramatically enhanced for even the trans isomer. This study shows a unique example in which spatial arrangement and dynamic properties can strongly influence molecular reactivity in unimolecular reactions, and it will be helpful for the future design of a reactive structure depending on dynamic conformational changes.
We propose an effective scheme for fast conformational searches by combining the replica exchange method (REM) with the generalized effect potential concept. The present method introduces the "q" ...value from the effective potential as a coupling parameter. It is found that the new method not only requires a much smaller number of replicas than the conventional REM, but also makes it possible to perform effective conformational sampling of complex systems with correct distributions maintained. The advantage of the present method has been demonstrated with in vacuo alanine dipeptide using a molecular dynamics simulation.
Time-dependent formulations of the reactive scattering theory based on the wavepacket correlation functions with the Møller wavepackets for the electronically nonadiabatic reactions are presented. ...The calculations of state-to-state reactive probabilities for the quasi-Jahn-Teller scattering model system were performed. The conical intersection (CI) effects are investigated by comparing the results of the two-surface nonadiabatic calculations and the single surface adiabatic approximation. It was found that the results of the two-surface nonadiabatic calculations show interesting features in the reaction probability due to the conical intersection. Single surface adiabatic calculations with extended Born-Oppenheimer approximation using simple wavepacket phase factor was found to be able to reproduce the CI effect semi-quantitatively, while the single surface calculations with the usual adiabatic approximation cannot describe the scattering process for the Jahn- Teller model correctly. KCI Citation Count: 1
We performed molecular dynamics simulations of self-assembled supramolecular nanotubules constructed from amphiphiles with bent-shaped rods. By systematically examining the structure from dimeric ...aggregates to the fully developed nanotubule, we identified the basic building block of the nanotubule and the optimal dimensions of its stable structure which are consistent with experimental findings. Moreover, we demonstrate that the cooperative interplay of different interactions drives aggregation by selecting and stabilizing the optimal self-assembled structures for various intermediates through a complex pathway. Additionally, contraction of the nanotubule, which accompanies the dehydration process, was observed upon heating. It is suggested that the optimal stability of the self-assembled aggregates is achieved by balancing entropic and enthalpic contributions, of which the ratio is a critical factor that drives the aggregation pathway.
Amyloid deposits of Aβ protein in neuronal cells are known to be a major symptom of Alzheimer’s disease. In particular, Aβ42 shows relatively high toxicity among the different Aβ isoforms, and its ...toxicity is thought to be because of its structural features. Recent ssNMR and cryo-EM experiments identified that Aβ42 shows an S-shaped triple-β structure, in contrast to the previously suggested U-shaped β-arch structure. In order to associate the high toxicity of Aβ42 with its structural features, it is essential to explain the conformational stability and aggregation mechanisms of this triple-β motif. We utilized several different simulation methods, including extensive straight molecular dynamics simulation, steered molecular dynamics simulation, and replica-exchange molecular dynamics simulation. The S-shaped triple-β motif showed remarkable structural stability because of its complex residual interactions that form stable hydrophobic cores. The triple-β structure of Aβ42 is primarily made up of three β-sheet regions and two hydrophobic cores formed between β-sheet regions. Our analysis of β-sheet rupture patterns between adjacent chains showed that its two hydrophobic cores have different degrees of stability, indicating a lock phase mechanism. Our analysis of the docking pathway of monomeric Aβ42 to the fibril motif using REMD simulations showed that each of the three β-sheet sequences plays a distinct role in the docking process by changing their conformational features. Our results provide an understanding for the stability and consequent high toxicity of the triple-β structure Aβ42.
Amyloid deposits of Aβ protein in neuronal cells are known to be a major symptom of Alzheimer's disease. In particular, Aβ
shows relatively high toxicity among the different Aβ isoforms, and its ...toxicity is thought to be because of its structural features. Recent ssNMR and cryo-EM experiments identified that Aβ
shows an S-shaped triple-β structure, in contrast to the previously suggested U-shaped β-arch structure. In order to associate the high toxicity of Aβ
with its structural features, it is essential to explain the conformational stability and aggregation mechanisms of this triple-β motif. We utilized several different simulation methods, including extensive straight molecular dynamics simulation, steered molecular dynamics simulation, and replica-exchange molecular dynamics simulation. The S-shaped triple-β motif showed remarkable structural stability because of its complex residual interactions that form stable hydrophobic cores. The triple-β structure of Aβ
is primarily made up of three β-sheet regions and two hydrophobic cores formed between β-sheet regions. Our analysis of β-sheet rupture patterns between adjacent chains showed that its two hydrophobic cores have different degrees of stability, indicating a lock phase mechanism. Our analysis of the docking pathway of monomeric Aβ
to the fibril motif using REMD simulations showed that each of the three β-sheet sequences plays a distinct role in the docking process by changing their conformational features. Our results provide an understanding for the stability and consequent high toxicity of the triple-β structure Aβ
.
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