Table Of Contents Page, PNAS Volume 121, Number 27
Special Feature
Physics Meets Machine Learning
Machine learning has been proposed as an alternative to theoretical modeling when
dealing with complex problems in biological physics. However, in this perspective,
we argue that a more successful approach is a proper combination of these two ...
Modeling complex physical dynamics is a fundamental task in science and engineering.
Traditional physics-based models are first-principled, explainable, and sample-efficient.
However, they often rely on strong modeling assumptions and expensive numerical ...
Humans and animals excel at generalizing from limited data, a capability yet to be
fully replicated in artificial intelligence. This perspective investigates generalization
in biological and artificial deep neural networks (DNNs), in both in-distribution
...
The prediction of protein 3D structure from amino acid sequence is a computational
grand challenge in biophysics and plays a key role in robust protein structure prediction
algorithms, from drug discovery to genome interpretation. The advent of AI models,
...
Predicting which proteins interact together from amino acid sequences is an important
task. We develop a method to pair interacting protein sequences which leverages the
power of protein language models trained on multiple sequence alignments (MSAs), such
...
Direct design of complex functional materials would revolutionize technologies ranging
from printable organs to novel clean energy devices. However, even incremental steps
toward designing functional materials have proven challenging. If the material is
...
Recent years witnessed the development of powerful generative models based on flows,
diffusion, or autoregressive neural networks, achieving remarkable success in generating
data from examples with applications in a broad range of areas. A theoretical ...
The population loss of trained deep neural networks often follows precise power-law
scaling relations with either the size of the training dataset or the number of parameters
in the network. We propose a theory that explains the origins of and connects ...
In the quest to model neuronal function amid gaps in physiological data, a promising
strategy is to develop a normative theory that interprets neuronal physiology as optimizing
a computational objective. This study extends current normative models, which ...
This Week in PNAS
Retrospective
Profile
View related content:
Commentaries
Letters
This article has a reply:
View the original article:
Indirect reciprocity undermines indirect reciprocity destabilizing large-scale cooperation
Brief Report
The essential role of U4 snRNP in pre-messenger RNA (mRNA) splicing has been well
established. In this study, we utilized an antisense morpholino oligonucleotide (AMO)
specifically targeting U4 snRNA to achieve functional knockdown of U4 snRNP in HeLa
...
Physical Sciences
Applied Mathematics
Biologically detailed models of brain circuitry are challenging to build and simulate
due to the large number of neurons, their complex interactions, and the many unknown
physiological parameters. Simplified mathematical models are more tractable, but ...
Networks involved in information processing often have their nodes arranged hierarchically,
with the majority of connections occurring in adjacent levels. However, despite being
an intuitively appealing concept, the hierarchical organization of large ...
Applied Physical Sciences
Morphogenesis is one of the most marvelous natural phenomena. The morphological characteristics
of biological organs develop through growth, which is often triggered by mechanical
force. In this study, we propose a bioinspired strategy for hydrogel ...
Biophysics and Computational Biology
Organisms often swim through density-stratified fluids. Here, we investigate the dynamics
of active particles swimming in fluid density gradients and report theoretical evidence
of taxis as a result of these gradients (densitaxis). Specifically, we ...
Chemistry
Under nonequilibrium conditions, inorganic systems can produce a wealth of life-like
shapes and patterns which, compared to well-formed crystalline materials, remain widely
unexplored. A seemingly simple example is the formation of salt deposits during ...
Sodium-ion batteries (SIBs) as one of the promising alternatives to lithium-ion batteries
have achieved remarkable progress in the past. However, the all-climate performance
is still very challenging for SIBs. Herein, 15-Crown-5 (15-C-5) is screened as an
...
Although mechanically interlocked molecules (MIMs) display unique properties and functions
associated with their intricate connectivity, limited assembly strategies are available
for their synthesis. Herein, we presented a synergistic assembly strategy ...
Dynamic protein structures are crucial for deciphering their diverse biological functions.
Two-dimensional infrared (2DIR) spectroscopy stands as an ideal tool for tracing rapid
conformational evolutions in proteins. However, linking spectral ...
A metabolic inhibitor blocks cellular fucosylation and enables production of afucosylated antibodies
The fucosylation of glycoproteins regulates diverse physiological processes. Inhibitors
that can control cellular levels of protein fucosylation have consequently emerged
as being of high interest. One area where inhibitors of fucosylation have gained ...
Earth, Atmospheric, and Planetary Sciences
Turbulent mixing in the ocean exerts an important control on the rate and structure
of the overturning circulation. However, the balance of processes underpinning this
mixing is subject to significant uncertainties, limiting our understanding of the
...
Rain formation is a critical factor governing the lifecycle and radiative forcing
of clouds and therefore it is a key element of weather and climate. Cloud microphysics–turbulence
interactions occur across a wide range of scales and are challenging to ...
The Toarcian Oceanic Anoxic Event (T-OAE; ~183 Mya) was a globally significant carbon-cycle
perturbation linked to widespread deposition of organic-rich sediments, massive volcanic
CO2 release, marine faunal extinction, sea-level rise, a crisis in ...
Environmental Sciences
We show that the Landsat and Sentinel-2 satellites can detect NO2 plumes from large point sources at 10 to 60 m pixel resolution in their blue and
ultrablue bands. We use the resulting NO2 plume imagery to quantify nitrogen oxides (NOx) emission rates for ...
Climate influences near-surface biogeochemical processes and thereby determines the
partitioning of carbon dioxide (CO2) in shale, and yet the controls on carbon (C) weathering fluxes remain poorly constrained.
Using a dataset that characterizes ...
Physics
Degeneracy and symmetry have a profound relation in quantum systems. Here, we report
gate-tunable subband degeneracy in PbTe nanowires with a nearly symmetric cross-sectional
shape. The degeneracy is revealed in electron transport by the absence of a ...
Active fluids composed of constituents that are constantly driven away from thermal
equilibrium can support spontaneous currents and can be engineered to have unconventional
transport properties. Here, we report the emergence of (meta)stable traveling ...
Social Sciences
Economic Sciences
Significant progress reconciling economic activities with a stable climate requires
radical and rapid technological change in multiple sectors. Here, we study the case
of the automotive industry’s transition to electric vehicles, which involved choosing
...
Psychological and Cognitive Sciences
As disasters increase due to climate change, population density, epidemics, and technology,
information is needed about postdisaster consequences for people’s mental health and
how stress-related mental disorders affect multiple spheres of life, including ...
Languages disfavor word forms containing sequences of similar or identical consonants,
due to the biomechanical and cognitive difficulties posed by patterns of this sort.
However, the specific evolutionary processes responsible for this phenomenon are not
...
Psychosocial experiences affect brain health and aging trajectories, but the molecular
pathways underlying these associations remain unclear. Normal brain function relies
on energy transformation by mitochondria oxidative phosphorylation (OxPhos). Two ...
Echolocating bats are among the most social and vocal of all mammals. These animals
are ideal subjects for functional MRI (fMRI) studies of auditory social communication
given their relatively hypertrophic limbic and auditory neural structures and their
...
Humans tend to spontaneously imitate others’ behavior, even when detrimental to the
task at hand. The action observation network (AON) is consistently recruited during
imitative tasks. However, whether automatic imitation is mediated by cortico-cortical
...
Social Sciences
In one of the first papers on the impact of early-life conditions on individuals’
health in older age, Barker and Osmond [Lancet, 327, 1077–1081 (1986)] show a strong positive relationship between infant mortality rates
in the 1920s and ischemic heart ...
Sustainability Science
Significant progress reconciling economic activities with a stable climate requires
radical and rapid technological change in multiple sectors. Here, we study the case
of the automotive industry’s transition to electric vehicles, which involved choosing
...
Biological Sciences
Applied Biological Sciences
Biologically detailed models of brain circuitry are challenging to build and simulate
due to the large number of neurons, their complex interactions, and the many unknown
physiological parameters. Simplified mathematical models are more tractable, but ...
Establishing modular binders as diagnostic detection agents represents a cost- and
time-efficient alternative to the commonly used binders that are generated one molecule
at a time. In contrast to these conventional approaches, a modular binder can be ...
Controlling the principal African malaria vector, the mosquito Anopheles gambiae, is considered essential to curtail malaria transmission. However, existing vector
control technologies rely on insecticides, which are becoming increasingly ineffective.
...
Biochemistry
A metabolic inhibitor blocks cellular fucosylation and enables production of afucosylated antibodies
The fucosylation of glycoproteins regulates diverse physiological processes. Inhibitors
that can control cellular levels of protein fucosylation have consequently emerged
as being of high interest. One area where inhibitors of fucosylation have gained ...
S100A1, a small homodimeric EF-hand Ca2+-binding protein (~21 kDa), plays an important regulatory role in Ca2+ signaling pathways involved in various biological functions including Ca2+ cycling and contractile performance in skeletal and cardiac myocytes. ...
Biophysics and Computational Biology
Proteins mediate their functions through chemical interactions; modeling these interactions,
which are typically through sidechains, is an important need in protein design. However,
constructing an all-atom generative model requires an appropriate scheme ...
HCN1-4 channels are the molecular determinants of the If/Ih current that crucially regulates cardiac and neuronal cell excitability. HCN dysfunctions
lead to sinoatrial block (HCN4), epilepsy (HCN1), and chronic pain (HCN2), widespread
medical conditions ...
Cell Biology
Psychosocial experiences affect brain health and aging trajectories, but the molecular
pathways underlying these associations remain unclear. Normal brain function relies
on energy transformation by mitochondria oxidative phosphorylation (OxPhos). Two ...
A dispersed cytoplasmic distribution of mitochondria is a hallmark of normal cellular
organization. Here, we have utilized the expression of exogenous Trak2 in mouse oocytes and embryos to disrupt the dispersed distribution of mitochondria
by driving them ...
Ecology
Indeterminacy of ecological networks—the unpredictability of ecosystem responses to
persistent perturbations—is an emergent property of indirect effects a species has
on another through interaction chains. Thus, numerous indirect pathways in large,
...
Evolution
Tibetan sheep were introduced to the Qinghai Tibet plateau roughly 3,000 B.P., making
this species a good model for investigating genetic mechanisms of high-altitude adaptation
over a relatively short timescale. Here, we characterize genomic structural ...
Genetics
In 1967, in this journal, Evelyn Witkin proposed the existence of a coordinated DNA
damage response in Escherichia coli, which later came to be called the “SOS response.” We revisited this response using
the replication inhibitor azidothymidine (AZT) and ...
The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic,
cultural, and political realignment in Western Europe. Here, we report the whole-genome
shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian
...
Immunology and Inflammation
Chronic inflammation is epidemiologically linked to the pathogenesis of gastrointestinal
diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC).
However, our understanding of the molecular mechanisms controlling gut inflammation
...
Asthma is a widespread airway disorder where GATA3-dependent Type-2 helper T (Th2)
cells and group 2 innate lymphoid cells (ILC2s) play vital roles. Asthma-associated
single nucleotide polymorphisms (SNPs) are enriched in a region located 926-970 kb
...
The non-neural cholinergic system plays a critical role in regulating immune equilibrium
and tissue homeostasis. While the expression of choline acetyltransferase (ChAT),
the enzyme catalyzing acetylcholine biosynthesis, has been well documented in ...
Immune checkpoint therapies (ICT) improve overall survival of patients with cancer
but may cause immune-related adverse events (irAEs) such as myocarditis. Cytotoxic
T lymphocyte-associated antigen 4 immunoglobulin fusion protein (CTLA-4 Ig), an inhibitor
...
Medical Sciences
Progerin, the protein that causes Hutchinson–Gilford progeria syndrome, triggers nuclear
membrane (NM) ruptures and blebs, but the mechanisms are unclear. We suspected that
the expression of progerin changes the overall structure of the nuclear lamina. ...
Microbiology
Maintenance of DNA integrity is essential to all forms of life. DNA damage generated
by reaction with genotoxic chemicals results in deleterious mutations, genome instability,
and cell death. Pathogenic bacteria encounter several genotoxic agents during ...
Type I toxin–antitoxin systems (T1TAs) are bipartite bacterial loci encoding a growth-inhibitory
toxin and an antitoxin small RNA (sRNA). In many of these systems, the transcribed
toxin mRNA is translationally inactive, but becomes translation-competent ...
Neuroscience
Networks involved in information processing often have their nodes arranged hierarchically,
with the majority of connections occurring in adjacent levels. However, despite being
an intuitively appealing concept, the hierarchical organization of large ...
Echolocating bats are among the most social and vocal of all mammals. These animals
are ideal subjects for functional MRI (fMRI) studies of auditory social communication
given their relatively hypertrophic limbic and auditory neural structures and their
...
Humans tend to spontaneously imitate others’ behavior, even when detrimental to the
task at hand. The action observation network (AON) is consistently recruited during
imitative tasks. However, whether automatic imitation is mediated by cortico-cortical
...
Enlargement of the cerebrospinal fluid (CSF)–filled brain ventricles (cerebral ventriculomegaly),
the cardinal feature of congenital hydrocephalus (CH), is increasingly recognized
among patients with autism spectrum disorders (ASD). KATNAL2, a member of ...
Spinal cord dorsal horn inhibition is critical to the processing of sensory inputs,
and its impairment leads to mechanical allodynia. How this decreased inhibition occurs
and whether its restoration alleviates allodynic pain are poorly understood. Here,
...
Coordination of goal-directed behavior depends on the brain’s ability to recover the
locations of relevant objects in the world. In humans, the visual system encodes the
spatial organization of sensory inputs, but neurons in early visual areas map objects
...
The spatial distribution of proteins and their arrangement within the cellular ultrastructure
regulates the opening of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
receptors in response to glutamate release at the synapse. Fluorescence ...
TMEM16F is a calcium-activated phospholipid scramblase and nonselective ion channel,
which allows the movement of lipids bidirectionally across the plasma membrane. While
the functions of TMEM16F have been extensively characterized in multiple cell types,
...
Physiology
The transient receptor potential melastatin (TRPM) tetrameric cation channels are
involved in a wide range of biological functions, from temperature sensing and taste
transduction to regulation of cardiac function, inflammatory pain, and insulin ...
To survive adverse environments, many animals enter a dormant state such as hibernation,
dauer, or diapause. Various Drosophila species undergo adult reproductive diapause in response to cool temperatures and/or
short day-length. While flies are less ...
Corrections
Cover image: Pictured is an artistic illustration of the interplay between AI and the natural world. A collection of articles in the Physics Meets Machine Learning Special Feature explores how advances in machine learning can help solve problems in the natural sciences and how ideas from physics and biology can help improve machine learning. Together, the articles highlight interconnected and emerging research in the topics of physics and machine learning, with applications including protein folding, material assembly, and neural networks. See the Introduction to the Special Feature, e2403580121. Image credit: Alex Eben Meyer for the Simons Foundation.
Sign up for PNAS alerts.
Get alerts for new articles, or get an alert when an article is cited.
Manage alertsStay connected
Submit to PNAS
Submit to the Proceedings of the National Academy of Sciences (PNAS) and have your research discovered by millions of researchers in the Biological, Physical, and Social Sciences.
Submit your manuscript