RESUMEN

In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other for the density fluctuation of water, by projecting all the mechanical variables in phase space onto the two dynamic variables: the structural fluctuation defined by the displacement of atoms from their equilibrium positions, and the solvent density fluctuation. The equation has an expression similar to the classical Langevin equation (CLE) for a harmonic oscillator, possessing terms corresponding to the restoring force proportional to the structural fluctuation, as well as the frictional and random forces. However, there is a distinct difference between the two expressions that touches on the essential physics of the structural fluctuation, that is, the force constant, or Hessian, in the restoring force. In the CLE, this is given by the second derivative of the potential energy among atoms in a protein. So, the quadratic nature or the harmonicity is only valid at the minimum of the potential surface. On the contrary, the linearity of the restoring force in the GLE originates from the projection of the water's degrees of freedom onto the protein's degrees of freedom. Taking this into consideration, Kim and Hirata proposed an ansatz for the Hessian matrix. The ansatz is used to equate the Hessian matrix with the second derivative of the free-energy surface or the potential of the mean force of a protein in water, defined by the sum of the potential energy among atoms in a protein and the solvation free energy. Since the free energy can be calculated from the molecular mechanics and the RISM/3D-RISM theory, one can perform an analysis similar to the normal mode analysis (NMA) just by diagonalizing the Hessian matrix of the free energy. This method is referred to as the Generalized Langevin Mode Analysis (GLMA). This theory may be realized to explore a variety of biophysical processes, including protein folding, spectroscopy, and chemical reactions. The present article is devoted to reviewing the development of this theory, and to providing perspective in exploring life phenomena.

Asunto(s)

Proteínas , Agua , Termodinámica , Proteínas/química , Solventes/química , Agua/química , Simulación de Dinámica Molecular

RESUMEN

The movement of individual weaver ants, of Oecophylla smargandina, was previously tracked within an unfamiliar arena. We develop an empirical model, based on Brownian motion with a linear drag and constant driving force, to explain the observed distribution of ants over position and velocity. Parameters are fixed according to the isotropic, homogeneous distribution observed near the middle of the arena. Then, with no adjustable parameters, the model accounts for all features of the measured population distribution. The tendency of ants to remain near arena edges is largely explained as a statistical property of bounded stochastic motion though evidence for active wall-following behavior appears in individual ant trajectories. Members of this ant species are capable of impressive feats of collective action and long-range navigation. But we argue that they use a simplistic algorithm, captured semi-quantitatively by the model provided, to navigate within the confined region.

RESUMEN

Dual frequency magnetic excitation of magnetic nanoparticles (MNP) enables enhanced biosensing applications. This was studied from an experimental and theoretical perspective: nonlinear sum-frequency components of MNP exposed to dual-frequency magnetic excitation were measured as a function of static magnetic offset field. The Langevin model in thermodynamic equilibrium was fitted to the experimental data to derive parameters of the lognormal core size distribution. These parameters were subsequently used as inputs for micromagnetic Monte-Carlo (MC)-simulations. From the hysteresis loops obtained from MC-simulations, sum-frequency components were numerically demodulated and compared with both experiment and Langevin model predictions. From the latter, we derived that approximately 90% of the frequency mixing magnetic response signal is generated by the largest 10% of MNP. We therefore suggest that small particles do not contribute to the frequency mixing signal, which is supported by MC-simulation results. Both theoretical approaches describe the experimental signal shapes well, but with notable differences between experiment and micromagnetic simulations. These deviations could result from Brownian relaxations which are, albeit experimentally inhibited, included in MC-simulation, or (yet unconsidered) cluster-effects of MNP, or inaccurately derived input for MC-simulations, because the largest particles dominate the experimental signal but concurrently do not fulfill the precondition of thermodynamic equilibrium required by Langevin theory.

RESUMEN

BACKGROUND: Magnetic nanoparticles (MNPs) have been proposed as drug carriers for targeted therapy. Noninvasive imaging methods that can compute the distribution of MNPs have also attracted much attention. METHOD: Based on the Langevin theory, the theoretical relationship between the magnetic force and the concentration of MNPs was derived. The acoustic pressure wave equation containing the concentration of MNPs was established. RESULT: The acoustic pressure waveform reflected the dimension and position of the MNPs region. From reconstructed images, MNPs regions with different concentrations and different sizes were clearly distinguished. CONCLUSION: The concentration of MNPs can be parsed from the acoustic signals generated by particles vibrations. This conclusion indicates that magneto-acoustic concentration tomography of magnetic nanoparticles with magnetic induction (MACT-MI) has potential to detect and reconstruct the concentration of MNPs in biological tissue.

Asunto(s)

Nanopartículas de Magnetita , Acústica , Fenómenos Magnéticos , Magnetismo , Tomografía

RESUMEN

We show that charge recombination in ordered heterojunctions depends sensitively on the degree of coherent delocalization of charges at the donor-acceptor interface. Depending on the relative sign of the electron and hole transfer integrals, such delocalization can dramatically suppress recombination through destructive quantum interference. This could explain why measured recombination rates are significantly lower than predictions based on Langevin theory for a variety of organic bulk heterojunctions. Moreover, it opens up a design strategy for photovoltaic devices with enhanced efficiencies through coherently suppressed charge recombination.