bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Март 22, 2023
Biomolecular
condensates
form
via
phase
transitions
of
condensate-specific
biomacromolecules.
Intrinsically
disordered
regions
(IDRs)
featuring
the
appropriate
sequence
grammar
can
contribute
homotypic
and
heterotypic
interactions
to
driving
forces
for
separation
multivalent
proteins.
At
this
juncture,
experiments
computations
have
matured
point
where
concentrations
coexisting
dense
dilute
phases
be
quantified
individual
IDRs
in
complex
milieus
both
vitro
vivo
.
For
a
macromolecule
such
as
protein
solvent,
locus
points
that
connects
two
defines
boundary
or
binodal.
Often,
only
few
along
binodal,
especially
phase,
are
accessible
measurement.
In
cases
quantitative
comparative
analysis
parameters
describe
separation,
it
is
useful
fit
measured
computed
binodals
well-known
mean-field
free
energies
polymer
solutions.
Unfortunately,
non-linearity
underlying
energy
functions
makes
challenging
put
theories
into
practice.
Here,
we
present
FIREBALL,
suite
computational
tools
designed
enable
efficient
construction,
analysis,
fitting
experimental
data
binodals.
We
show
depending
on
theory
being
used,
one
also
extract
information
regarding
coil-to-globule
macromolecules.
emphasize
ease-of-use
utility
FIREBALL
using
examples
based
different
IDRs.Macromolecular
drives
assembly
membraneless
bodies
known
biomolecular
condensates.
Measurements
computer
simulations
now
brought
bear
quantify
how
macromolecules
vary
with
changes
solution
conditions.
These
mappings
analytical
expressions
assessments
balance
macromolecule-solvent
across
systems.
However,
non-linear
them
actual
non-trivial.
To
numerical
analyses,
introduce
user-friendly
allows
generate,
analyze,
diagrams
theories.
Physical review. B./Physical review. B,
Год журнала:
2025,
Номер
111(5)
Опубликована: Фев. 27, 2025
We
propose
an
analytical
thermodynamic
model
for
describing
defect
phase
transformations,
which
we
term
the
statistical
evaluation
approach
(SPEA).
The
SPEA
assumes
a
Boltzmann
distribution
of
finite-size
fractions
and
calculates
their
average.
To
benchmark
performance
model,
apply
it
to
construct
binary
surface
diagrams
metal
alloys.
Two
alloy
systems
are
considered:
Mg
with
Ca
substitutions
Ni
Nb
substitutions.
firm
basis
against
can
be
leveled,
first
perform
Monte
Carlo
(MC)
simulations
coupled
cluster
expansion
density
functional
theory
dataset.
then
demonstrate
that
reproduces
MC
results
accurately.
Specifically,
correctly
predicts
order-disorder
transitions
as
well
coexistence
1/3
ordered
disordered
phase.
Finally,
compare
method
sublattice
commonly
used
in
CALPHAD
describe
random
solution
phases
transitions.
proposed
provides
highly
efficient
modeling
transformations.
Published
by
American
Physical
Society
2025
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Март 6, 2025
Protein
responses
to
environmental
stress,
particularly
temperature
fluctuations,
have
long
been
a
subject
of
investigation,
with
focus
on
how
proteins
maintain
homeostasis
and
exhibit
thermoresponsive
properties.
While
UCST-type
(upper
critical
solution
temperature)
phase
behavior
has
studied
extensively
can
now
be
predicted
reliably
using
computational
models,
LCST-type
(lower
transitions
remain
less
explored,
lack
models
capable
accurate
prediction.
This
gap
limits
our
ability
probe
fully
undergo
in
response
changes.
Here,
we
introduce
Mpipi-T,
residue-level
coarse-grained
model
designed
predict
proteins.
Parametrized
both
atomistic
simulations
experimental
data,
Mpipi-T
accounts
for
entropically
driven
protein
separation
that
occurs
upon
heating.
Accordingly,
predicts
temperature-driven
quantitatively
single-
multi-chain
systems.
Beyond
its
predictive
capabilities,
demonstrate
provides
framework
uncovering
the
molecular
mechanisms
underlying
heat
stress
responses,
offering
new
insights
into
sense
adapt
thermal
changes
biological
Advanced Materials,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 10, 2025
Biopolymers
and
bioinspired
materials
contribute
to
the
construction
of
intricate
hierarchical
structures
that
exhibit
advanced
properties.
The
remarkable
toughness
damage
tolerance
such
multilevel
are
conferred
through
assembly
their
multiscale
(i.e.,
atomistic
macroscale)
components
architectures.
Here,
functionality
mechanisms
biopolymers
bio-inspired
at
multilength
scales
explored
summarized,
focusing
on
biopolymer
nanofibril
configurations,
biocompatible
synthetic
biopolymers,
composites.
Their
modeling
methods
with
theoretical
basis
multiple
lengths
time
reviewed
for
applications.
Additionally,
exploration
artificial
intelligence-powered
methodologies
is
emphasized
realize
improvements
in
these
from
functionality,
biodegradability,
sustainability
characterization,
fabrication
process,
superior
designs.
Ultimately,
a
promising
future
versatile
manufacturing
across
wider
applications
greater
lifecycle
impacts
foreseen.
Vestnik Moskovskogo Universiteta Seriya 3 Fizika Astronomiya,
Год журнала:
2025,
Номер
80(№1, 2025)
Опубликована: Янв. 1, 2025
In
this
work,
a
phase
diagram
of
the
neighborhood
triple
point
one-component
system
in
van
der
Waals
approximation
is
constructed.
It
shown
that
makes
it
possible
to
describe
corresponding
coexistence
three
aggregate
states
matter
–
solid,
liquid
and
gaseous.
The
possibility
using
for
points
other
types
discussed.
Materials Horizons,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
This
study
represents
a
novel
methodology
utilizing
quantum
support
vector
classifier
to
predict
phase
diagrams
in
quinary
systems
which
enhances
predictive
accuracy
beyond
classical
methods.
The Journal of Chemical Physics,
Год журнала:
2025,
Номер
162(18)
Опубликована: Май 8, 2025
Phase
diagrams
are
crucial
to
the
design
of
new
materials,
understand
their
phase
stability
and
metastability
under
different
thermodynamic
conditions,
such
as
composition,
temperature,
pressure.
Here,
we
use
an
ab
initio
approach
study
diagram
a
binary
alloy
within
low
concentration
limit
solute.
Using
molecular
dynamics
calculations
based
on
density
functional
theory,
estimate
solute
partitioning
ratios
in
solid–liquid
equilibria.
The
chemical
potential
difference
between
solvent
atoms
both
solid
liquid
phases
is
calculated
using
integration.
As
illustration
techniques,
have
applied
this
method
reproduce
Al–Mg
at
zero
We
also
compute
coexistence
curve
pure
Al
by
applying
phase-coexistence
with
free
energy
correction
technique.
results
close
agreement
experiment,
demonstrating
reliability
models.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Май 10, 2025
Abstract
Machine
learning
interatomic
potentials
(MLIPs)
have
become
a
workhorse
of
modern
atomistic
simulations,
and
recently
published
universal
MLIPs,
pre-trained
on
large
datasets,
demonstrated
remarkable
accuracy
generalizability.
However,
the
computational
cost
MLIPs
limits
their
applicability
to
chemically
disordered
systems
requiring
simulation
cells
or
sample-intensive
statistical
methods.
Here,
we
report
use
continuous
differentiable
alchemical
degrees
freedom
in
materials
exploiting
fact
that
graph
neural
network
represent
discrete
elements
as
real-valued
tensors.
The
proposed
method
introduces
atoms
with
corresponding
weights
into
input
graph,
alongside
modifications
message-passing
readout
mechanisms
allows
smooth
interpolation
between
compositional
states
materials.
end-to-end
differentiability
enables
efficient
calculation
gradient
energy
respect
weights.
With
this
modification,
propose
methodologies
for
optimizing
composition
solid
solutions
towards
target
macroscopic
properties,
characterizing
order
disorder
multicomponent
oxides,
conducting
free
simulations
quantify
vacancy
formation
changes.