Results 61 to 70 of about 2,903,061 (286)

A light‐triggered Time‐Resolved X‐ray Solution Scattering (TR‐XSS) workflow with application to protein conformational dynamics

FEBS Open Bio, EarlyView.
Time‐resolved X‐ray solution scattering captures how proteins change shape in real time under near‐native conditions. This article presents a practical workflow for light‐triggered TR‐XSS experiments, from data collection to structural refinement. Using a calcium‐transporting membrane protein as an example, the approach can be broadly applied to study ...
Fatemeh Sabzian‐Molaei, Fredrik Orädd, Konstantinos Magkakis, Magnus Andersson   +3 more
wiley   +1 more source

TorchSim: an efficient atomistic simulation engine in PyTorch

AI for Science
We introduce TorchSim, an open-source atomistic simulation engine tailored for the machine learned interatomic potential (MLIP) era. By rewriting core atomistic simulation primitives in PyTorch, TorchSim can achieve orders of magnitude acceleration for ...
Orion Cohen, Janosh Riebesell, Rhys Goodall, Adeesh Kolluru, Stefano Falletta, Joseph Krause, Jorge Colindres, Gerbrand Ceder, Abhijeet S Gangan   +8 more
doaj   +1 more source

Computational Study of Crystallography, Defects, Ion Migration and Dopants in Almandine Garnet

Physchem, 2022
Almandine garnet has received considerable amounts of interest due to its application in manufacturing and engineering processes. Defect processes, Fe-ion diffusion pathways, and promising dopants on the Al, Fe, and Si sites are examined using classical ...
Janya Lumbini Subasinghe, Sashikesh Ganeshalingam, Navaratnarajah Kuganathan   +2 more
doaj   +1 more source

Iterative methods for the force-based quasicontinuum approximation : analysis of a 1D model problem [PDF]

, 2011
Force-based atomistic-continuum hybrid methods are the only known pointwise consistent methods for coupling a general atomistic model to a finite-element continuum model.
Luskin, Mitchell Barry, Ortner, C., Ortner, Christoph, M. Dobson, M. Luskin, C. Ortner, Luskin, M., Dobson, Matthew   +7 more
core   +1 more source

Refinement of amino‐acid conformation vs. difference density maps in time‐resolved serial femtosecond crystallography data analysis

FEBS Open Bio, EarlyView.
The dFoCC pipeline starts with observed DED and resting‐state coordinates, which are then used to generate a library of triggered states. Correlation analysis of the calculated DED features of each candidate vs observed DED permits quantitative evaluation of candidate structural quality.
Meng Iao Fong, Yuhei Hosokawa, Lars Oliver Essen, Manuel Maestre‐Reyna   +3 more
wiley   +1 more source

Molecular characterization of covRS mutations in M1UK Streptococcus pyogenes

FEBS Open Bio, EarlyView.
Group A Streptococcus (GAS) acquires covRS mutations driving a hypervirulent bacterial state, frequently associated with invasive disease‐like necrotizing fasciitis. We demonstrate that the newly emerged M1UK GAS lineage can also acquire these mutations.
Jarrad Pritchard, Emma‐Jayne Proctor, Jiawa Wang, Nikolas P. Johnston, Andrew Hayes, Georgia McCorkell, Haibo Yu, Jai Tree, Mark R. Davies, Mark J. Walker, Ronald Sluyter, Stephan Brouwer, Martina L. Sanderson‐Smith   +12 more
wiley   +1 more source

Malformin A1–mediated cytotoxicity in ovarian cancer cells occurs through pyroptosis and autophagy

FEBS Open Bio, EarlyView.
This study investigated the effects of the natural compound Malformin A1 (MA1) on the cytoskeleton that regulates cell proliferation and migration. Disruption of the cytoskeleton can impair these processes and promote cancer cell death. MA1 disrupted cytoskeletal organization, induced DNA damage, inflammation, activated autophagy, and pyroptosis ...
Nada Abdullah Hassan, Ikram A. Burney, Shika Hanif Malgundkar, Siva Ramamoorthy, Ressin Varghese, Mohamed A. Al‐Kindi, Hamad Al Riyami, Shadia Al Bahlani, Sergey Dobretsov, Syed Imran Hassan, Benjamin K. Tsang, Yahya Tamimi   +11 more
wiley   +1 more source

Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure.

PLoS ONE, 2019
Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of formation of these phases and transitions between them are computationally prohibitive, hence ...
Saeed Mortezazadeh, Yousef Jamali, Hossein Naderi-Manesh, Alexander P Lyubartsev   +3 more
doaj   +1 more source

Structural studies and functional engineering of NanX: an anhydro‐sialic acid transporter from Escherichia coli

FEBS Open Bio, EarlyView.
Biophysical characterisation shows that NanX, a membrane transport protein from the major facilitator superfamily (MFS), forms both monomers and dimers after purification. AlphaFold modelling and substrate docking provide information on residues likely involved in substrate recognition for NanX and another MFS member, NanT.
Michael C. Newton‐Vesty, Kelsi R. Hall, Zachary D. Tillett, Liam S. Turk, James S. Davies, Michael J. Currie, Hamish G. Brown, Sepideh Valimehr, Peter D. Mace, Andrew E. Whitten, Santosh Panjikar, Eric Hanssen, Rachel A. North, Renwick C.J. Dobson   +13 more
wiley   +1 more source

Multiscale simulation of heat transfer in a rarefied gas [PDF]

, 2014
We present a new hybrid method for dilute gas flows that couples a continuum- fluid description to the direct simulation Monte Carlo (DSMC) technique.
Borg, Matthew Karl, Lockerby, Duncan A., Docherty, Stephanie, Reese, Jason   +3 more
core   +4 more sources