7,144 research outputs found
Out-of-equilibrium collective oscillation as phonon condensation in a model protein
In the first part of the present paper (theoretical), the activation of
out-of-equilibrium collective oscillations of a macromolecule is described as a
classical phonon condensation phenomenon. If a macromolecule is modeled as an
open system, that is, it is subjected to an external energy supply and is in
contact with a thermal bath to dissipate the excess energy, the internal
nonlinear couplings among the normal modes make the system undergo a
non-equilibrium phase transition when the energy input rate exceeds a threshold
value. This transition takes place between a state where the energy is
incoherently distributed among the normal modes, to a state where the input
energy is channeled into the lowest frequency mode entailing a coherent
oscillation of the entire molecule. The model put forward in the present work
is derived as the classical counterpart of a quantum model proposed long time
ago by H. Fr\"ohlich in the attempt to explain the huge speed of enzymatic
reactions. In the second part of the present paper (experimental), we show that
such a phenomenon is actually possible. Two different and complementary THz
near-field spectroscopic techniques, a plasmonic rectenna, and a micro-wire
near-field probe, have been used in two different labs to get rid of artefacts.
By considering a aqueous solution of a model protein, the BSA (Bovine Serum
Albumin), we found that this protein displays a remarkable absorption feature
around 0.314 THz, when driven in a stationary out-of-thermal equilibrium state
by means of optical pumping. The experimental outcomes are in very good
qualitative agreement with the theory developed in the first part, and in
excellent quantitative agreement with a theoretical result allowing to identify
the observed spectral feature with a collective oscillation of the entire
molecule.Comment: 49 pages, 10 figures; Physical Review X, (2018) in pres
Vibrational Density Matrix Renormalization Group
Variational approaches for the calculation of vibrational wave functions and
energies are a natural route to obtain highly accurate results with
controllable errors. However, the unfavorable scaling and the resulting high
computational cost of standard variational approaches limit their application
to small molecules with only few vibrational modes. Here, we demonstrate how
the density matrix renormalization group (DMRG) can be exploited to optimize
vibrational wave functions (vDMRG) expressed as matrix product states. We study
the convergence of these calculations with respect to the size of the local
basis of each mode, the number of renormalized block states, and the number of
DMRG sweeps required. We demonstrate the high accuracy achieved by vDMRG for
small molecules that were intensively studied in the literature. We then
proceed to show that the complete fingerprint region of the sarcosyn-glycin
dipeptide can be calculated with vDMRG.Comment: 21 pages, 5 figures, 4 table
The development of biomolecular Raman optical activity spectroscopy
Following its first observation over 40 years ago, Raman optical activity (ROA), which may be measured as a small difference in the intensity of vibrational Raman scattering from chiral molecules in right- and left-circularly polarized incident light or, equivalently, the intensity of a small circularly polarized component in the scattered light using incident light of fixed polarization, has evolved into a powerful chiroptical spectroscopy for studying a large range of biomolecules in aqueous solution. The long and tortuous path leading to the first observations of ROA in biomolecules in 1989, in which the author was closely involved from the very beginning, is documented, followed by a survey of subsequent developments and applications up to the present day. Among other things, ROA provides information about motif and fold, as well as secondary structure, of proteins; solution structure of carbohydrates; polypeptide and carbohydrate structure of intact glycoproteins; new insight into structural elements present in unfolded protein sequences; and protein and nucleic acid structure of intact viruses. Quantum chemical simulations of observed Raman optical activity spectra provide the complete three-dimensional structure, together with information about conformational dynamics, of smaller biomolecules. Biomolecular ROA measurements are now routine thanks to a commercial instrument based on a novel design becoming available in 2004
Collective behavior of oscillating electric dipoles
The present work reports about the dynamics of a collection of randomly
distributed, and randomly oriented, oscillators in 3D space, coupled by an
interaction potential falling as , where r stands for the inter-particle
distance. This model schematically represents a collection of identical
biomolecules, coherently vibrating at some common frequency, coupled with a
potential stemming from the electrodynamic interaction between
oscillating dipoles. The oscillating dipole moment of each molecule being a
direct consequence of its coherent (collective) vibration. By changing the
average distance among the molecules, neat and substantial changes in the power
spectrum of the time variation of a collective observable are found. As the
average intermolecular distance can be varied by changing the concentration of
the solvated molecules, and as the collective variable investigated is
proportional to the projection of the total dipole moment of the model
biomolecules on a coordinate plane, we have found a prospective experimental
strategy of spectroscopic kind to check whether the mentioned intermolecular
electrodynamic interactions can be strong enough to be detectable, and thus to
be of possible relevance to biology.Comment: 20 pages, 4 figure
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