441 research outputs found
Dynamic Self-Organization and Catalysis: Periodic versus Random Driving Forces
No full textDynamic
self-assembly is an emerging area of research where properly
designed self-assembly elements can be used reversibly to trigger
and control some tasks at the molecular level. The interactions between
decorated nanoparticles, NPs, are experimentally modifiable by a variety
of stimuli that can also vary in time periodically or randomly. In
coarse-grained simulations, we activate a switch, either periodically
or randomly, which assembles–disassembles clusters of NPs.
We then introduce a single catalytic NP(C) covered with catalytic
moieties, C, and leave all remaining NP(R)s decorated with reactive
moieties, R. The catalytic reaction that converts R into products
P depends on the encounter of C and R. Particle-based simulations
are here used to study the catalytic activity and reaction yields
of decorated nanoparticles that aggregate/disaggregate with the application
of time-varying perturbations. Static aggregation is not catalytically
efficient because it traps the catalyst. The application of random
perturbations that vary in time in the form of colored noises improves
the reaction yields and can provide opportunities for more efficient
catalytic activity. The work can also allow us to understand how in
Nature many biological processes are affected or driven by random/noisy
fluctuations of the environment
Polaritonic Chemistry: Hindering and Easing Ground State Polyenic Isomerization via Breakdown of σ-π Separation
No full textThe ground state conformational isomerization in polyenes is a symmetry allowed process. Its low energy barrier is governed by electron density transfer from the formal single bond that is rotated to the nearby formal double bonds. Along the reaction pathway, the transition state is therefore destabilized. The rules of polaritonic chemistry, i.e., chemistry in a nanocavity with reflecting windows, are barely beginning to be laid out. The standing electric field of the nanocavity couples strongly with the molecular wave function and modifies the potential energy curve in unexpected ways. A quantum electrodynamics approach, applied to the torsional degree of freedom of the central bond of butadiene, shows that formation of the polariton mixes the sigma-pi frameworks thereby stabilizing/destabilizing the planar, reactant-like conformations. The values of the fundamental mode of the cavity field used in the absence of the cavity do not trigger this mechanism
Hydrodynamic fluctuations in the presence of one parameter Mittag-Leffler friction
No full textThe effects of hydrodynamic fluctuations on the subdiffusive motion of a particle subject to one parameter Mittag-Leffler friction are examined by means of the fractional Langevin equation. The particle experiences an overall additive colored noise formed by, on the one hand, the hydrodynamic back flow effects and, on the other hand, an additional contribution predicted by fluctuation dissipation relation. Particle motion may or may not be subject to a restoring force. All possible combinations of forces exerted on the test particle are being studied, and for each of them the generalized response function in terms of multinomial Mittag-Leffler functions is provided. Mean square displacement, normalized velocity and position auto-correlation functions are furnished as special cases of the generalized response function, and their short and long time limits are analytically given. In addition, for the same measures analytical expressions valid for time windows much broader than the usual asymptotic limit are provided, and can be used to fit real life data. We demonstrate that normalized velocity and position auto-correlation functions are the main sources providing information on the effect of hydrodynamic fluctuations on particle motion. Actually, they oppose to friction and to restoring force, and smooth out the anti-persistent character of the motion
Electric Field Effects on Short Fibrils of A beta Amyloid Peptides
No full textAmyloid fibrils are highly ordered protein aggregates, which are associated with many neurodegenerative diseases. The assembling dynamics of monomeric beta-amyloid peptides, A beta, into small aggregates (and then into long fibrils) is still debated and has become a hot topic. In this study, we conducted molecular dynamics simulations in explicit water of small A beta protofibrils (from monomer to pentamer) under the perturbation of an externally applied electric field with the aim of investigating the fundamental molecular interactions involved in the aggregation mechanism. Dynamics of small adducts of A beta(16-42) in the presence of an electric field, which was shown before to accelerate the conformational change of a single molecule, indicate that the structural resilience increases with the number of molecules in the aggregate. In particular, for 50 ns, the pentamer shows an enhanced stability in secondary structure, number of hydrogen bonds, and number of salt bridges, even in the presence of the field perturbation. The resilience to the field perturbation is linked to the variation of the induced dipole moment of the aggregates that tends to level off very rapidly with the growing number of molecules, thereby reducing the energy available per molecule to produce structural changes. The results also show that in the presence of the field the stability of the hydrophobic second beta-sheet (32, residues 31-42) is higher than that of the first one (beta 1, residues 18-26). In particular, we identify Gly33, Gly37, and Met35 as the most important residues that stabilize the intermolecular packing and may act as nucleation sites for fibrillization. Furthermore, dynamics of the full-length A beta(1-42) pentameric aggregate, which include the highly charged random coil residues 1-15, confirmed the key role of the second hydrophobic core in the protofibril structure
Role of the intracellular cavity in potassium channel conductivity
No full textThe role of several fragments of the potassium channel KcsA has been examined by the Poisson-Nernst-Planck (PNP) theory. The efficiency of the computational method allowed comparing a large number of channel models, with different intracellular gate openings, partial atomic charges, and amino acid sequences. Perhaps counter-intuitively, the calculated ion current decreases when the mean radius of the entrance cavity increases. Widening of the vestibule, in fact, increases the volume accessible to water, which is the volume with a high dielectric constant. In turn, water screens the attractive charges of the P-loop backbone. The backbone charges of the M2 helixes instead oppose the entrance of potassium ions through a complicated mechanism that can be separated in the activity of two interfering dipoles. The conductance of the KcsA models increased when two neutral residues in M2 were mutated to glutamic acid, in agreement with experimental results (Brelidze, T. I.; Niu, X.; Magleby, K. L. PNAS 2003, 100, 9017-9022). As a general conclusion, a relation between channel conductance and potassium concentration in the intracellular cavity emerged. Although the ion transport is the result of the fine balance of a number of different effects, the experimental results can be reproduced quantitatively only on the basis of electrostatic forces, which are the only driving forces modeled by the PNP theory
Molecules on Gold surfaces: what they do and how they go around to do it
No full textA review of the computational models that describe the interactions of molecules on gold surface
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