A structural biology compatible file format for atomic force microscopy
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Фев. 15, 2025
Cryogenic
electron
microscopy
(cryo-EM),
X-ray
crystallography,
and
nuclear
magnetic
resonance
(NMR)
contribute
structural
data
that
are
interchangeable,
cross-verifiable,
visualizable
on
common
platforms,
making
them
powerful
tools
for
our
understanding
of
protein
structures.
Unfortunately,
atomic
force
(AFM)
has
so
far
failed
to
interface
with
these
biology
methods,
despite
the
recent
development
localization
AFM
(LAFM)
allows
extracting
high-resolution
information
from
data.
Here,
we
build
LAFM
develop
a
pipeline
transforms
into
3D-density
files
(.afm)
readable
by
programs
commonly
used
visualize,
analyze,
interpret
We
show
3D-LAFM
densities
can
serve
as
fields
steer
molecular
dynamics
flexible
fitting
(MDFF)
obtain
models
previously
unresolved
states
based
observations
in
close-to-native
environment.
Besides,
.afm
format
enables
direct
3D
or
2D
visualization
analysis
conventional
images.
anticipate
file
will
find
wide
usage
embed
repertoire
methods
routinely
community,
allowing
researchers
deposit
repositories
comparison
cross-verification
other
techniques.
Язык: Английский
AI-Enabled Compact and Efficient Dynamic Light Scattering System for Precise Microparticle Sizing
Applied Sciences,
Год журнала:
2025,
Номер
15(4), С. 1900 - 1900
Опубликована: Фев. 12, 2025
A
cost-effective
and
efficient
AI-DLS
framework
integrating
dynamic
light
scattering
(DLS)
with
artificial
intelligence
(AI)
enables
precise
microparticle
size
characterization.
compact
DLS
system
was
developed
using
a
helium–neon
laser,
high-frequency
photodetectors,
optimized
optical
components,
achieving
significant
miniaturization—4.5%
volume,
16.7%
weight,
25%
cost
of
conventional
systems.
Advanced
signal
processing,
such
as
Kalman
filtering,
improved
data
quality,
while
deep
learning
models
(deep
neural
network
(DNN),
one-dimensional
convolutional
(1D-CNN),
2D-CNN
Gramian
angular
field
transformations)
enhanced
prediction
accuracy.
The
model
achieved
exceptional
results,
mean
absolute
error
10
nm
99%
matched
the
stability
accuracy
traditional
instruments,
reducing
test
time
by
80%.
This
scalable,
low-cost
solution
overcomes
limitations,
offering
broad
accessibility
for
scientific
industrial
Язык: Английский
Mechanisms of pore geometry and apparent morphology on the wettability of coal-ionic liquids
Physics of Fluids,
Год журнала:
2025,
Номер
37(2)
Опубликована: Фев. 1, 2025
In
order
to
investigate
the
mechanism
of
pore
regulation
on
wetting
performance
coal-ionic
liquids,
and
liquids
at
different
temperatures
were
analyzed
based
contact
angle,
surface
tension,
low-field
nuclear
magnetic
resonance,
atomic
force
microscopy
experiments.
A
method
comprehensively
analyzing
through
structure
morphology
was
proposed.
The
findings
demonstrated
that
properties
ionic
coal
showed
temperature
selectivity,
with
containing
Cl−
preferring
low
[BMIM][BF4]
contrary.
After
treatment,
average
diameter,
roughness,
porosity
samples
increased
by
0.34–18.36
nm,
2.09–9.7
0.5929%–1.4313%,
respectively,
trend
parameter
change
aligns
characteristic
change.
addition,
fitting
results
revealed
increase
in
roughness
had
a
negative
correlation
angle's
size
positive
porosity,
indicating
can
affect
changing
apparent
coal.
research
are
significant
enhancing
mine
dust
management
capability.
Язык: Английский
Quantitative study on the interfacial performance of micron-fiber cord/elastomer
Composites Part B Engineering,
Год журнала:
2025,
Номер
unknown, С. 112625 - 112625
Опубликована: Май 1, 2025
Язык: Английский
Perspectives Toward an Integrative Structural Biology Pipeline With Atomic Force Microscopy Topographic Images
Journal of Molecular Recognition,
Год журнала:
2024,
Номер
37(6)
Опубликована: Сен. 27, 2024
After
the
recent
double
revolutions
in
structural
biology,
which
include
use
of
direct
detectors
for
cryo-electron
microscopy
resulting
a
significant
improvement
expected
resolution
large
macromolecule
structures,
and
advent
AlphaFold
allows
near-accurate
prediction
any
protein
field
biology
is
now
pursuing
more
ambitious
targets,
including
several
MDa
assemblies.
But
complex
target
systems
cannot
be
tackled
using
single
biophysical
technique.
The
integrative
has
emerged
as
global
solution.
aim
to
integrate
data
from
multiple
complementary
techniques
produce
final
three-dimensional
model
that
obtained
absence
atomic
force
platforms
not
necessarily
due
its
nm
resolution,
opposed
Å
x-ray
crystallography,
nuclear
magnetic
resonance,
or
electron
microscopy.
Rather
issue
was
AFM
topographic
lacked
interpretability.
Fortunately,
with
introduction
AFM-Assembly
pipeline
other
similar
tools,
it
possible
into
modeling
platforms.
advantages
molecule
techniques,
such
AFM,
ability
confirm
experimentally
assembled
molecular
models
alternative
conformations
mimic
inherent
flexibility
proteins
complexes.
review
begins
brief
overview
historical
developments
followed
by
an
examination
strengths
limitations
imaging,
have
hindered
integration
modern
This
discusses
correction
images,
well
principles
behind
pipeline.
It
also
presents
series
challenges
need
addressed
order
improve
incorporation
platform.
Язык: Английский
Advances and Challenges in Interfacial Binding Forces for Electrocatalysts
ChemSusChem,
Год журнала:
2024,
Номер
unknown
Опубликована: Июль 9, 2024
As
a
practical
chemical
energy
conversion
technology,
electrocatalysis
could
be
used
in
fields
of
and
environmental
protection.
In
recent
years,
significant
research
efforts
have
been
devoted
to
the
design
development
high-performance
electrocatalysts
because
rational
catalysts
is
crucial
for
enhancing
electrocatalytic
performance.
Creating
by
forming
interactions
between
different
components
at
interface
an
important
means
controlling
improving
Therefore,
several
common
interfacial
binding
forces
synthesizing
was
systematically
summarized
this
review
first
time.
The
discussion
revolves
around
roles
these
play
various
reaction
processes.
Various
characterization
techniques
capable
proving
existence
also
involved
review.
Finally,
some
prospects
challenges
designing
researching
materials
through
utilization
were
presented.
Язык: Английский
Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy
Structure,
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 1, 2024
Язык: Английский
Pro-inflammatory S100A8 Protein Exhibits a Detergent-like Effect on Anionic Lipid Bilayers, as Imaged by High-Speed AFM
ACS Applied Materials & Interfaces,
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 26, 2024
Neuronal
cell
death
induced
by
membrane
damage
is
one
of
the
major
hallmarks
neurodegenerative
diseases.
Neuroinflammation
precedes
loss
neurons;
however,
whether
and
how
inflammation-related
proteins
contribute
to
integrity
remains
unknown.
We
employed
a
range
biophysical
tools,
including
high-speed
atomic
force
microscopy,
fluorescence
spectroscopy,
electrochemical
impedance
ascertain
pro-inflammatory
protein
S100A8
induces
alterations
in
biomimetic
lipid
membranes
upon
interaction.
Our
findings
underscore
crucial
roles
played
divalent
cations
charge.
found
that
apo-S100A8
selectively
interacts
with
anionic
composed
phosphatidylserine
(PS),
causing
disruption
through
detergent-like
mechanism,
primarily
affecting
regions
where
phospholipids
are
less
tightly
packed.
Interestingly,
introduction
Ca2+
ions
inhibited
S100A8-induced
disruption,
suggesting
disruptive
effects
most
pronounced
under
conditions
mimicking
intracellular
compartments,
calcium
levels
low,
PS
concentrations
inner
leaflet
high.
Overall,
our
results
present
mechanistic
basis
for
understanding
molecular
interactions
between
plasma
membrane,
emphasizing
as
potential
contributor
onset
Язык: Английский