The Journal of Chemical Physics,
Journal Year:
2025,
Volume and Issue:
162(16)
Published: April 22, 2025
Enhanced
sampling
simulations
help
overcome
free
energy
barriers
and
explore
molecular
conformational
space
by
applying
external
bias
potential
along
suitable
collective
variables
(CVs).
However,
identifying
optimal
CVs
that
align
with
the
slow
modes
of
complex
systems
many
coupled
degrees
freedom
can
be
a
significant
challenge.
Deep
time-lagged
independent
component
analysis
(Deep-TICA)
addresses
this
issue
employing
an
artificial
neural
network
generates
non-linear
combinations
descriptors
to
learn
slowest
freedom.
Training
Deep-TICA
CVs,
however,
typically
requires
long
equilibrium
sample
multiple
recrossing
events
across
various
metastable
conformations
molecule.
This
requirement
often
prohibitively
expensive,
thereby
limiting
its
widespread
application.
In
study,
we
present
algorithm
enables
training
using
limited
amount
trajectory
data
obtained
from
short,
non-equilibrium
metadynamics
only
one
forward
transition
initial
final
state.
We
achieve
utilizing
variational
Koopman
algorithm,
which
reweights
short
off-equilibrium
trajectories
reflect
probability
densities.
demonstrate
enhanced
conducted
reweighted
CV
accurately
efficiently
converge
surface
for
such
as
Müller–Brown
potential,
alanine
dipeptide,
chignolin
mini-protein.
Our
approach,
therefore,
key
challenge
inferring
data,
making
it
more
feasible
use
deep
learning
study
processes
practical
relevance.
ACS Catalysis,
Journal Year:
2024,
Volume and Issue:
14(3), P. 1252 - 1256
Published: Jan. 10, 2024
Among
the
many
catalysts
suggested
for
ammonia
decomposition,
Li2NH
has
been
shown
to
be
quite
promising.
In
recent
past,
we
have
performed
extensive
ab
initio-quality
simulations
explain
workings
of
this
unusual
catalyst.
complex
scenario
that
emerged,
surface
dynamics
and
structural
disorder
enhanced
by
interaction
with
reacting
molecules
played
crucial
roles.
Non-stoichiometric
lithium
imide
(Li2–x(NH2)x(NH)1–x)
reported
better
catalytic
performances
than
pure
imide.
Stimulated
these
findings,
follow
up
our
previous
study
simulating
decomposition
on
such
non-stoichiometric
compounds.
We
attribute
reactivity
fact
compositional
further
enhances
fluctuations
in
topmost
layers
catalyst,
strengthening
dynamic
picture
process.
The Journal of Physical Chemistry Letters,
Journal Year:
2024,
Volume and Issue:
15(6), P. 1774 - 1783
Published: Feb. 8, 2024
Enhanced-sampling
algorithms
relying
on
collective
variables
(CVs)
are
extensively
employed
to
study
complex
(bio)chemical
processes
that
not
amenable
brute-force
molecular
simulations.
The
selection
of
appropriate
CVs
characterizing
the
slow
movement
modes
is
paramount
importance
for
reliable
and
efficient
enhanced-sampling
In
this
Perspective,
we
first
review
application
limitations
obtained
from
chemical
geometrical
intuition.
We
also
introduce
path-sampling
algorithms,
which
can
identify
path-like
in
a
high-dimensional
free-energy
space.
Machine-learning
offer
viable
approach
finding
suitable
by
analyzing
trajectories
preliminary
discuss
both
performance
machine-learning-derived
simulations
experimental
models
challenges
involved
applying
these
realistic,
assemblies.
Moreover,
provide
prospective
view
potential
advancements
machine-learning
development
field
The Journal of Chemical Physics,
Journal Year:
2025,
Volume and Issue:
162(9)
Published: March 4, 2025
In
computational
physics,
chemistry,
and
biology,
the
implementation
of
new
techniques
in
shared
open-source
software
lowers
barriers
to
entry
promotes
rapid
scientific
progress.
However,
effectively
training
users
presents
several
challenges.
Common
methods
like
direct
knowledge
transfer
in-person
workshops
are
limited
reach
comprehensiveness.
Furthermore,
while
COVID-19
pandemic
highlighted
benefits
online
training,
traditional
tutorials
can
quickly
become
outdated
may
not
cover
all
software’s
functionalities.
To
address
these
issues,
here
we
introduce
“PLUMED
Tutorials,”
a
collaborative
model
for
developing,
sharing,
updating
tutorials.
This
initiative
utilizes
repository
management
continuous
integration
ensure
compatibility
with
updates.
Moreover,
interconnected
form
structured
learning
path
enriched
automatic
annotations
provide
broader
context.
paper
illustrates
development,
features,
advantages
PLUMED
Tutorials,
aiming
foster
an
open
community
creating
sharing
educational
resources.
The Journal of Chemical Physics,
Journal Year:
2024,
Volume and Issue:
160(17)
Published: May 2, 2024
Several
enhanced
sampling
techniques
rely
on
the
definition
of
collective
variables
to
effectively
explore
free
energy
landscapes.
The
existing
that
describe
progression
along
a
reactive
pathway
offer
an
elegant
solution
but
face
number
limitations.
In
this
paper,
we
address
these
challenges
by
introducing
new
path-like
variable
called
“deep-locally
non-linear-embedding,”
which
is
inspired
principles
locally
linear
embedding
technique
and
trained
trajectory.
mimics
ideal
reaction
coordinate
automatically
generating
non-linear
combination
features
through
differentiable
generalized
autoencoder
combines
neural
network
with
continuous
k-nearest
neighbor
selection.
Among
key
advantages
method
its
capability
choose
metric
for
searching
neighbors
learn
path
from
state
A
B
without
need
handpick
landmarks
priori.
We
demonstrate
effectiveness
DeepLNE
showing
closely
approximates
in
toy
models,
such
as
Müller-Brown
potential
alanine
dipeptide.
Then,
use
it
molecular
dynamics
simulations
RNA
tetraloop,
where
highlight
accelerate
transitions
estimate
folding.
PNAS Nexus,
Journal Year:
2024,
Volume and Issue:
3(4)
Published: March 28, 2024
A
variety
of
enhanced
sampling
(ES)
methods
predict
multidimensional
free
energy
landscapes
associated
with
biological
and
other
molecular
processes
as
a
function
few
selected
collective
variables
(CVs).
The
accuracy
these
is
crucially
dependent
on
the
ability
chosen
CVs
to
capture
relevant
slow
degrees
freedom
system.
For
complex
processes,
finding
such
real
challenge.
Machine
learning
(ML)
offer,
in
principle,
solution
handle
this
problem.
However,
rely
availability
high-quality
datasets-ideally
incorporating
information
about
physical
pathways
transition
states-which
are
difficult
access,
therefore
greatly
limiting
their
domain
application.
Here,
we
demonstrate
how
datasets
can
be
generated
by
means
ES
simulations
trajectory
space
via
metadynamics
paths
algorithm.
approach
expected
provide
general
efficient
way
generate
ML-based
for
fast
prediction
simulations.
We
our
two
numerical
examples,
2D
model
potential
isomerization
alanine
dipeptide,
using
deep
targeted
discriminant
analysis
CV
choice.
Journal of Chemical Theory and Computation,
Journal Year:
2024,
Volume and Issue:
20(11), P. 4523 - 4532
Published: May 27, 2024
Rare
event
sampling
is
a
central
problem
in
modern
computational
chemistry
research.
Among
the
existing
methods,
transition
path
(TPS)
can
generate
unbiased
representations
of
reaction
processes.
However,
its
efficiency
depends
on
ability
to
reactive
trial
paths,
which
turn
quality
shooting
algorithm
used.
We
propose
new
based
success
rate,
i.e.,
reactivity,
measured
as
function
reduced
set
collective
variables
(CVs).
These
are
extracted
with
machine
learning
approach
directly
from
TPS
simulations,
using
multitask
objective
function.
Iteratively,
this
workflow
significantly
improves
without
any
prior
knowledge
process.
In
addition,
optimized
CVs
be
used
biased
enhanced
methodologies
accurately
reconstruct
free
energy
profiles.
tested
method
three
different
systems:
two-dimensional
toy
model,
conformational
transitions
alanine
dipeptide,
and
hydrolysis
acetyl
chloride
bulk
water.
latter,
we
integrated
our
an
active
scheme
learn
learning-based
potential,
allowed
us
study
mechanism
profile
ab
initio-like
accuracy.
Journal of Chemical Theory and Computation,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Feb. 4, 2025
Most
enhanced
sampling
methods
facilitate
the
exploration
of
molecular
free
energy
landscapes
by
applying
a
bias
potential
along
reduced
dimensional
collective
variable
(CV)
space.
The
success
these
depends
on
ability
CVs
to
follow
relevant
slow
modes
system.
Intuitive
CVs,
such
as
distances
or
contacts,
often
prove
inadequate,
particularly
in
biological
systems
involving
many
coupled
degrees
freedom.
Machine
learning
algorithms,
especially
neural
networks
(NN),
can
automate
process
CV
discovery
combining
large
number
descriptors
and
outperform
intuitive
efficiency.
However,
their
lack
interpretability
high
cost
evaluation
during
trajectory
propagation
make
NN-CVs
difficult
apply
biomolecular
processes.
Here,
we
introduce
surrogate
model
approach
using
lasso
regression
express
output
network
linear
combination
an
automatically
chosen
subset
input
descriptors.
We
demonstrate
successful
applications
our
simulation
conformational
landscape
alanine
dipeptide
chignolin
mini-protein.
In
addition
providing
mechanistic
insights
due
explainable
nature,
showed
negligible
loss
efficiency
accuracy,
compared
NN-CVs,
reconstructing
underlying
surface.
Moreover,
simplified
functional
forms,
are
better
at
extrapolating
unseen
regions
space,
e.g.,
saddle
points.
Surrogate
also
less
expensive
evaluate
NN
counterparts,
making
them
suitable
for
complex
Biochimica et Biophysica Acta (BBA) - General Subjects,
Journal Year:
2023,
Volume and Issue:
1868(2), P. 130534 - 130534
Published: Dec. 6, 2023
The
relevance
of
motions
in
biological
macromolecules
has
been
clear
since
the
early
structural
analyses
proteins
by
X-ray
crystallography.
Computer
simulations
have
applied
to
provide
a
deeper
understanding
dynamics
1976,
and
are
now
standard
tool
many
labs
working
on
structure
function
biomolecules.
In
this
mini-review
we
highlight
some
areas
current
interest
active
development
for
simulations,
particular
all-atom
molecular
simulations.