Biophysical Journal
@biophysj.bsky.social
The premier journal of quantitative biology and leading journal for molecular, cellular, and systems biophysics research. Editor-in-Chief: Vasanthi Jayaraman.
#OPENACCESS: Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition. Kumar Gaurav, Virginia Busetto, Diego Javier Páez-Moscoso, Arya Changiarath, Sonya M. Hanson, Sebastian Falk, René F. Ketting, and Lukas S. Stelzl.
Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition
Phase separation of proteins plays a critical role in cellular organization. How phase-separated protein condensates underpin biological function and how condensates achieve specificity remain…
www.cell.com
November 26, 2025 at 3:04 PM
#OPENACCESS: Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition. Kumar Gaurav, Virginia Busetto, Diego Javier Páez-Moscoso, Arya Changiarath, Sonya M. Hanson, Sebastian Falk, René F. Ketting, and Lukas S. Stelzl.
#OPENACCESS: Chromatin unfolding via loops can drive clustered transposon insertion. Roshan Prizak, Aaron Gadzekpo, and Lennart Hilbert.
Chromatin unfolding via loops can drive clustered transposon insertion
Transposons, DNA sequences capable of relocating within the genome, make up a significant portion of eukaryotic genomes and are often found in clusters. Within the cell nucleus, the genome is…
www.cell.com
November 25, 2025 at 7:02 PM
#OPENACCESS: Chromatin unfolding via loops can drive clustered transposon insertion. Roshan Prizak, Aaron Gadzekpo, and Lennart Hilbert.
New study by Arjun Valiya Parambathu et al. (2025) uncovers why concentrated mAbs get so gooey—it’s like a crowded dance floor where every antibody keeps bumping, sticking, and slowing the groove. High viscosity = molecular traffic jam!
Molecular origins of high viscosity in concentrated solutions of monoclonal antibodies
Concentrated monoclonal antibody (mAb) solutions can allow subcutaneous administration of effective doses of the therapeutic, but for some mAbs this leads to anomalously high viscosities; mAb-mAb…
www.cell.com
November 25, 2025 at 3:02 PM
New study by Arjun Valiya Parambathu et al. (2025) uncovers why concentrated mAbs get so gooey—it’s like a crowded dance floor where every antibody keeps bumping, sticking, and slowing the groove. High viscosity = molecular traffic jam!
#OPENACCESS: Transformer graph variational autoencoder for generative molecular design. Trieu Nguyen and Aleksandra Karolak.
Transformer graph variational autoencoder for generative molecular design
In the field of drug discovery, the generation of new molecules with desirable properties remains a critical challenge. Traditional methods often rely on simplified molecular input line entry system…
www.cell.com
November 24, 2025 at 7:02 PM
#OPENACCESS: Transformer graph variational autoencoder for generative molecular design. Trieu Nguyen and Aleksandra Karolak.
The authors present a simulation toolbox designed to project membrane and biopolymer properties to a two-dimensional plane. The dimension reduction helps to characterize the patterns of lipid-lipid and lipid-biopolymer surfaces.
2Danalysis: A toolbox for analysis of lipid membranes and biopolymers in two-dimensional space
Molecular simulations expand our ability to learn about the interplay of biomolecules. Biological membranes, composed of diverse lipids with varying physicochemical properties, are highly dynamic…
www.cell.com
November 24, 2025 at 3:03 PM
The authors present a simulation toolbox designed to project membrane and biopolymer properties to a two-dimensional plane. The dimension reduction helps to characterize the patterns of lipid-lipid and lipid-biopolymer surfaces.
#OPENACCESS: A single molecular switch controls the clock – New study using Markovian state models maps the conformational landscape of CK1, revealing how kinase shape tunes substrate specificity and circadian timing.
www.cell.com
November 21, 2025 at 7:03 PM
#OPENACCESS: A single molecular switch controls the clock – New study using Markovian state models maps the conformational landscape of CK1, revealing how kinase shape tunes substrate specificity and circadian timing.
Special issue call for papers: Modeling Biology at Multiple Scales: From Macromolecules to Cells, Dedicated to Jie Liang.
www.biophysics.org
November 21, 2025 at 2:31 PM
Special issue call for papers: Modeling Biology at Multiple Scales: From Macromolecules to Cells, Dedicated to Jie Liang.
New study by Deng Li et al. (2025) shows how SP-D grabs glycans using a slick new computational workflow—like watching a molecular claw machine finally reveal its strategy. Precision, pattern-spotting, and plenty of biophysical flair!
www.cell.com
November 20, 2025 at 7:02 PM
New study by Deng Li et al. (2025) shows how SP-D grabs glycans using a slick new computational workflow—like watching a molecular claw machine finally reveal its strategy. Precision, pattern-spotting, and plenty of biophysical flair!
A brand-new MD algorithm tailored to sample the protein intermediate states, termed as ‘discard-and-restart’, enhancing the design of ligands targeting dynamic protein states.
www.cell.com
November 20, 2025 at 3:02 PM
A brand-new MD algorithm tailored to sample the protein intermediate states, termed as ‘discard-and-restart’, enhancing the design of ligands targeting dynamic protein states.
Special issue call for papers: Martin Karplus: In Memoriam.
www.biophysics.org
November 19, 2025 at 8:30 PM
Special issue call for papers: Martin Karplus: In Memoriam.
#OPENACCESS: Structural and functional characterization of the Pro64Ser leptin mutant: Implications for congenital leptin deficiency. Bao Quoc Ngo, Outi Lampela, and André H. Juffer.
www.cell.com
November 19, 2025 at 7:04 PM
#OPENACCESS: Structural and functional characterization of the Pro64Ser leptin mutant: Implications for congenital leptin deficiency. Bao Quoc Ngo, Outi Lampela, and André H. Juffer.
Many ligands, many sites. Orr et al. combine experiments and simulations to show how drugs and excipients bind multiple sites on human serum albumin, with important implications for improved therapeutic formulations.
www.cell.com
November 19, 2025 at 3:02 PM
Many ligands, many sites. Orr et al. combine experiments and simulations to show how drugs and excipients bind multiple sites on human serum albumin, with important implications for improved therapeutic formulations.
Read about the cover art for the newly released issue of Biophysical Journal on the BPS Blog: www.biophysics.org/blog/harness...
Harnessing Molecular Simulations and Artificial Intelligence to Advance Biomass Pretreatment and Biobased Materials Manufacturing
We are excited to share the cover image of the November 18 issue of Biophysical Journal, capturing the complex association between biomass polymers—cellulose, hemicellulose, and lignin. The image is a...
www.biophysics.org
November 18, 2025 at 3:48 PM
Read about the cover art for the newly released issue of Biophysical Journal on the BPS Blog: www.biophysics.org/blog/harness...
#OPENACCESS: Packing of apolar amino acids is not a strong stabilizing force in transmembrane helix dimerization. Gilbert J. Loiseau and Alessandro Senes.
Packing of apolar amino acids is not a strong stabilizing force in transmembrane helix dimerization
The factors that stabilize the folding and oligomerization of membrane proteins are still not well understood. In particular, it remains unclear how the tight and complementary packing between apolar…
www.cell.com
November 17, 2025 at 7:02 PM
#OPENACCESS: Packing of apolar amino acids is not a strong stabilizing force in transmembrane helix dimerization. Gilbert J. Loiseau and Alessandro Senes.
Memory in motion. Li et al. use an active vertex model to show how polarity memory in confined cell collectives drives coherent cell rotation and period reversals in migration directions.
Time-dependent active force drives periodic reversal in collective cell migration
Collective cell migration is prevalent in the processes of embryo development, wound healing, and cancer metastasis across various space and time scales. Although various motion modes have been…
www.cell.com
November 17, 2025 at 3:03 PM
Memory in motion. Li et al. use an active vertex model to show how polarity memory in confined cell collectives drives coherent cell rotation and period reversals in migration directions.
#OPENACCESS: Spatiotemporal dynamics of local anesthetic diffusion in nerve revealed by a 2D computational model. Vladimir Smrkolj, Jakob Kralj, Janez Mavri, and Nejc Umek.
Spatiotemporal dynamics of local anesthetic diffusion in nerve revealed by a 2D computational model
Despite their extensive clinical use, the intraneural pharmacokinetics of local anesthetics, including the mechanisms determining their onset and duration, remain incompletely understood,…
www.cell.com
November 14, 2025 at 7:02 PM
#OPENACCESS: Spatiotemporal dynamics of local anesthetic diffusion in nerve revealed by a 2D computational model. Vladimir Smrkolj, Jakob Kralj, Janez Mavri, and Nejc Umek.
#OPENACCESS: Annotating the x-ray diffraction pattern of vertebrate striated muscle. Natalia A. Koubassova, Debabrata Dutta, Weikang Ma, Andrey K. Tsaturyan, Thomas Irving, Raúl Padrón, and Roger Craig.
Annotating the x-ray diffraction pattern of vertebrate striated muscle
Low-angle x-ray diffraction is a powerful technique for analyzing the molecular structure of the myofilaments of striated muscle in situ. It has contributed greatly to our understanding of the…
www.cell.com
November 14, 2025 at 3:03 PM
#OPENACCESS: Annotating the x-ray diffraction pattern of vertebrate striated muscle. Natalia A. Koubassova, Debabrata Dutta, Weikang Ma, Andrey K. Tsaturyan, Thomas Irving, Raúl Padrón, and Roger Craig.
Cells rolling in microvessels = like shopping carts with varying wheel grip. Yonggang Li et al. (2025) link molecular bond dynamics to how fast cells “roll” in blood flow. Tiny stickiness = big traffic effects!
A cross-scale analysis for the determinants of bonding dynamics on the distributions of rolling velocities of cells in microvessels
The interplay between subcellular adhesion dynamics and cellular-scale deformations under shear flow drives key physiological and pathological processes. Whereas both bond kinetics and fluid-cell…
www.cell.com
November 13, 2025 at 7:03 PM
Cells rolling in microvessels = like shopping carts with varying wheel grip. Yonggang Li et al. (2025) link molecular bond dynamics to how fast cells “roll” in blood flow. Tiny stickiness = big traffic effects!
Special issue call for papers: Viral Biophysics.
www.biophysics.org
November 13, 2025 at 2:30 PM
Special issue call for papers: Viral Biophysics.
The authors present initial experimental evidence detailing the biophysical mechanisms by which SARS-CoV-2 interferes with pulmonary surfactant function, highlighting the role of the S2 subunit of the viral spike protein in inducing this inhibition.
Biophysical mechanisms of SARS-CoV-2-induced surfactant inhibition
Surfactant replacement has been studied as a supportive therapy for managing COVID-19-induced acute respiratory distress syndrome. The clinical applications require biophysical understanding of the…
www.cell.com
November 12, 2025 at 7:03 PM
The authors present initial experimental evidence detailing the biophysical mechanisms by which SARS-CoV-2 interferes with pulmonary surfactant function, highlighting the role of the S2 subunit of the viral spike protein in inducing this inhibition.
#OPENACCESS: Reactive oxygen species counteract zebrafish wound contraction and promote wound healing. Chang Ding, Linlin Li, Yueyang Wang, Hong-Anh A. Nguyen, Deva D. Chan, David M. Umulis, Adrian T. Buganza, and Qing Deng.
Reactive oxygen species counteract zebrafish wound contraction and promote wound healing
Reactive oxygen species (ROS) are second messengers that drive wound closure. However, the mechanism by which ROS regulate wound contraction to facilitate wound healing remains unclear. Here, we…
www.cell.com
November 12, 2025 at 3:03 PM
#OPENACCESS: Reactive oxygen species counteract zebrafish wound contraction and promote wound healing. Chang Ding, Linlin Li, Yueyang Wang, Hong-Anh A. Nguyen, Deva D. Chan, David M. Umulis, Adrian T. Buganza, and Qing Deng.
In the New and Notable "Milestone for the interpretation of muscle x-ray diffraction patterns," Anthony L. Hessel highlights the paper "Annotating the X-ray diffraction pattern of vertebrate striated muscle."
Milestone for the interpretation of muscle x-ray diffraction patterns
Research on mammalian cardiac and skeletal muscle spans fields such as exercise physiology, longevity science, and inherited myopathies. Muscle is composed of many repeating contractile units, called…
www.cell.com
November 11, 2025 at 7:04 PM
In the New and Notable "Milestone for the interpretation of muscle x-ray diffraction patterns," Anthony L. Hessel highlights the paper "Annotating the X-ray diffraction pattern of vertebrate striated muscle."
#OPENACCESS: Nayak et al. develop a computational whole-cell model revealing how actin-microtubule crosstalk drives cell polarity, shape, and migration behaviors.
Modeling actin-microtubule crosstalk in migrating cells
Actin-microtubule crosstalk regulates the polarity and morphology of migrating cells and encompasses mechanical interactions, mediated by cross-linkers, molecular motors, and cytoskeletal regulators.…
www.cell.com
November 11, 2025 at 3:04 PM
#OPENACCESS: Nayak et al. develop a computational whole-cell model revealing how actin-microtubule crosstalk drives cell polarity, shape, and migration behaviors.
#OPENACCESS: The study reveals key features of the different structural states of the 5 ‘and 3’ UTRs of the dengue virus during its replication, highlighting the adaptability of the UTR structures and contributing to the development of targeted drugs. buff.ly/dtWrfLJ
Structural dynamics of dengue virus UTRs and their cyclization
The dengue virus (DENV) poses a significant threat to human health, accounting for approximately 400 million infections each year. Its genome features a circular structure that facilitates…
www.cell.com
November 10, 2025 at 7:02 PM
#OPENACCESS: The study reveals key features of the different structural states of the 5 ‘and 3’ UTRs of the dengue virus during its replication, highlighting the adaptability of the UTR structures and contributing to the development of targeted drugs. buff.ly/dtWrfLJ
#OPENACCESS: MreB filaments in the elongasome modulate E. coli membrane curvature. Becca W.A. Baileeves, Anthony D.Q. Hoang, Timothy D.H. Bugg, and Phillip J. Stansfeld.
MreB filaments in the elongasome modulate E. coli membrane curvature
MreB, a bacterial actin homolog, plays a pivotal role in defining the shape of rod-shaped bacteria by coordinating peptidoglycan synthesis during cell elongation. It forms filaments that interact…
www.cell.com
November 10, 2025 at 3:04 PM
#OPENACCESS: MreB filaments in the elongasome modulate E. coli membrane curvature. Becca W.A. Baileeves, Anthony D.Q. Hoang, Timothy D.H. Bugg, and Phillip J. Stansfeld.