754 research outputs found
Non-equilibrium phenomena and molecular reaction dynamics: mode space, energy space and conformer space
status: publishe
A parallel multistate framework for atomistic non-equilibrium reaction dynamics of solutes in strongly interacting organic solvents
We describe a parallel linear-scaling computational framework developed to
implement arbitrarily large multi-state empirical valence bond (MS-EVB)
calculations within CHARMM. Forces are obtained using the Hellman-Feynmann
relationship, giving continuous gradients, and excellent energy conservation.
Utilizing multi-dimensional Gaussian coupling elements fit to CCSD(T)-F12
electronic structure theory, we built a 64-state MS-EVB model designed to study
the F + CD3CN -> DF + CD2CN reaction in CD3CN solvent. This approach allows us
to build a reactive potential energy surface (PES) whose balanced accuracy and
efficiency considerably surpass what we could achieve otherwise. We use our PES
to run MD simulations, and examine a range of transient observables which
follow in the wake of reaction, including transient spectra of the DF
vibrational band, time dependent profiles of vibrationally excited DF in CD3CN
solvent, and relaxation rates for energy flow from DF into the solvent, all of
which agree well with experimental observations. Immediately following
deuterium abstraction, the nascent DF is in a non-equilibrium regime in two
different respects: (1) it is highly excited, with ~23 kcal mol-1 localized in
the stretch; and (2) not yet Hydrogen bonded to the CD3CN solvent, its
microsolvation environment is intermediate between the non-interacting
gas-phase limit and the solution-phase equilibrium limit. Vibrational
relaxation of the nascent DF results in a spectral blue shift, while relaxation
of its microsolvation environment results in a red shift. These two competing
effects result in a post-reaction relaxation profile distinct from that
observed when DF vibration excitation occurs within an equilibrium
microsolvation environment. The parallel software framework presented in this
paper should be more broadly applicable to a range of complex reactive systems.Comment: 58 pages and 29 Figure
Subtle Sensing:Detecting Differences in the Flexibility of Virtually Simulated Molecular Objects
During VR demos we have performed over last few years, many participants (in
the absence of any haptic feedback) have commented on their perceived ability
to 'feel' differences between simulated molecular objects. The mechanisms for
such 'feeling' are not entirely clear: observing from outside VR, one can see
that there is nothing physical for participants to 'feel'. Here we outline
exploratory user studies designed to evaluate the extent to which participants
can distinguish quantitative differences in the flexibility of VR-simulated
molecular objects. The results suggest that an individual's capacity to detect
differences in molecular flexibility is enhanced when they can interact with
and manipulate the molecules, as opposed to merely observing the same
interaction. Building on these results, we intend to carry out further studies
investigating humans' ability to sense quantitative properties of VR
simulations without haptic technology
Danceroom spectroscopy: At the frontiers of physics, performance, interactive art and technology
© 2016 ISAST. Danceroom Spectroscopy is an interactive audiovisual art installation and performance system driven by rigorous algorithms commonly used to simulate and analyze nanoscale atomic dynamics. danceroom Spectroscopy interprets humans as “energy landscapes,” resulting in an interactive system in which human energy fields are embedded within a simulation of thousands of atoms. Users are able to sculpt the atomic dynamics using their movements and experience their interactions visually and sonically in real time. danceroom Spectroscopy has so far been deployed as both an interactive sci-art installation and as the platform for a dance performance called Hidden Fields
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