8,433 research outputs found
Non-equilibrium phenomena and molecular reaction dynamics: mode space, energy space and conformer space
status: publishe
Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model
Here we present a systematic study of supercoil formation in DNA minicircles
under varying linking number by using molecular dynamics simulations of a
two-bead coarse-grained model. Our model is designed with the purpose of
simulating long chains without sacrificing the characteristic structural
properties of the DNA molecule, such as its helicity, backbone directionality
and the presence of major and minor grooves. The model parameters are extracted
directly from full-atomistic simulations of DNA oligomers via Boltzmann
inversion, therefore our results can be interpreted as an extrapolation of
those simulations to presently inaccessible chain lengths and simulation times.
Using this model, we measure the twist/writhe partitioning in DNA minicircles,
in particular its dependence on the chain length and excess linking number. We
observe an asymmetric supercoiling transition consistent with experiments. Our
results suggest that the fraction of the linking number absorbed as twist and
writhe is nontrivially dependent on chain length and excess linking number.
Beyond the supercoiling transition, chains of the order of one persistence
length carry equal amounts of twist and writhe. For longer chains, an
increasing fraction of the linking number is absorbed by the writhe.Comment: 21 pages, 7 figures, 1 tabl
Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters
This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a general message. First, we introduce a general method of hyperspherical mode analysis to analyze the energy transfer among internal modes of polyatomic molecules. In this method, the (3n−6) internal modes of an n-atom molecule are classified generally into three coarse level gyration-radius modes, three fine level twisting modes, and (3n−12) fine level shearing modes. We show that a large amount of kinetic energy flows into the gyration-radius modes when the cluster undergoes structural transitions by changing its mass distribution. Based on this fact, we construct a reactive mode as a linear combination of the three gyration-radius modes. It is shown that before the reactive mode acquires a large amount of kinetic energy, activation or inactivation of the twisting modes, depending on the geometry of the isomer, plays crucial roles for the onset of a structural transition. Specifically, in a symmetric isomer with a spherical mass distribution, activation of specific twisting modes drives the structural transition into an elongated isomer by inducing a strong internal centrifugal force, which has the effect of elongating the mass distribution of the system. On the other hand, in an elongated isomer, inactivation of specific twisting modes initiates the structural transition into a symmetric isomer with lower potential energy by suppressing the elongation effect of the internal centrifugal force and making the effects of the potential force dominant. This driving mechanism for reactions as well as the present method of hyperspherical mode analysis should be widely applicable to molecular reactions in which a system changes its overall mass distribution in a significant way
Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex
A remarkable amount of theoretical research has been carried out to elucidate
the physical origins of the recently observed long-lived quantum coherence in
the electronic energy transfer process in biological photosynthetic systems.
Although successful in many respects, several widely used descriptions only
include an effective treatment of the protein-chromophore interactions. In this
work, by combining an all-atom molecular dynamics simulation, time-dependent
density functional theory, and open quantum system approaches, we successfully
simulate the dynamics of the electronic energy transfer of the
Fenna-Matthews-Olson pigment-protein complex. The resulting characteristic
beating of populations and quantum coherences is in good agreement with the
experimental results and the hierarchy equation of motion approach. The
experimental absorption, linear and circular dichroism spectra and dephasing
rates are recovered at two different temperatures. In addition, we provide an
extension of our method to include zero-point fluctuations of the vibrational
environment. This work thus presents one of the first steps to explain the role
of excitonic quantum coherence in photosynthetic light-harvesting complexes
based on their atomistic and molecular description.Comment: 24 pages, 6 figure
Ultrafast charge transfer and vibronic coupling in a laser-excited hybrid inorganic/organic interface
Hybrid interfaces formed by inorganic semiconductors and organic molecules are intriguing materials for opto-electronics. Interfacial charge transfer is primarily responsible for their peculiar electronic structure and optical response. Hence, it is essential to gain insight into this fundamental process also beyond the static picture. Ab initio methods based on real-time time-dependent density-functional theory coupled to the Ehrenfest molecular dynamics scheme are ideally suited for this problem. We investigate a laser-excited hybrid inorganic/organic interface formed by the electron acceptor molecule 2,3,5,6-tetrafluoro-7,7,8,8-tetracyano-quinodimethane (F4TCNQ) physisorbed on a hydrogenated silicon cluster, and we discuss the fundamental mechanisms of charge transfer in the ultrashort time window following the impulsive excitation. The considered interface is p-doped and exhibits charge transfer in the ground state. When it is excited by a resonant laser pulse, the charge transfer across the interface is additionally increased, but contrary to previous observations in all-organic donor/acceptor complexes, it is not further promoted by vibronic coupling. In the considered time window of 100 fs, the molecular vibrations are coupled to the electron dynamics and enhance intramolecular charge transfer. Our results highlight the complexity of the physics involved and demonstrate the ability of the adopted formalism to achieve a comprehensive understanding of ultrafast charge transfer in hybrid materials
Some Further Results for the Stationary Points and Dynamics of Supercooled Liquids
We present some new theoretical and computational results for the stationary
points of bulk systems. First we demonstrate how the potential energy surface
can be partitioned into catchment basins associated with every stationary point
using a combination of Newton-Raphson and eigenvector-following techniques.
Numerical results are presented for a 256-atom supercell representation of a
binary Lennard-Jones system. We then derive analytical formulae for the number
of stationary points as a function of both system size and the Hessian index,
using a framework based upon weakly interacting subsystems. This analysis
reveals a simple relation between the total number of stationary points, the
number of local minima, and the number of transition states connected on
average to each minimum. Finally we calculate two measures of localisation for
the displacements corresponding to Hessian eigenvectors in samples of
stationary points obtained from the Newton-Raphson-based geometry optimisation
scheme. Systematic differences are found between the properties of eigenvectors
corresponding to positive and negative Hessian eigenvalues, and localised
character is most pronounced for stationary points with low values of the
Hessian index.Comment: 16 pages, 2 figure
Inferring diffusion in single live cells at the single molecule level
The movement of molecules inside living cells is a fundamental feature of
biological processes. The ability to both observe and analyse the details of
molecular diffusion in vivo at the single molecule and single cell level can
add significant insight into understanding molecular architectures of diffusing
molecules and the nanoscale environment in which the molecules diffuse. The
tool of choice for monitoring dynamic molecular localization in live cells is
fluorescence microscopy, especially so combining total internal reflection
fluorescence (TIRF) with the use of fluorescent protein (FP) reporters in
offering exceptional imaging contrast for dynamic processes in the cell
membrane under relatively physiological conditions compared to competing single
molecule techniques. There exist several different complex modes of diffusion,
and discriminating these from each other is challenging at the molecular level
due to underlying stochastic behaviour. Analysis is traditionally performed
using mean square displacements of tracked particles, however, this generally
requires more data points than is typical for single FP tracks due to
photophysical instability. Presented here is a novel approach allowing robust
Bayesian ranking of diffusion processes (BARD) to discriminate multiple complex
modes probabilistically. It is a computational approach which biologists can
use to understand single molecule features in live cells.Comment: combined ms (1-37 pages, 8 figures) and SI (38-55, 3 figures
Ab initio molecular dynamics study of liquid methanol
We present a density-functional theory based molecular-dynamics study of the
structural, dynamical, and electronic properties of liquid methanol under
ambient conditions. The calculated radial distribution functions involving the
oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare
well with recent neutron diffraction data, except for an underestimate of the
oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic
data, the hydroxyl stretching mode is significantly red-shifted in the liquid.
A substantial enhancement of the dipole moment is accompanied by significant
fluctuations due to thermal motion. Our results provide valuable data for
improvement of empirical potentials.Comment: 14 pages, 4 figures, accepted for publication in Chemical Physics
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