Accurately simulating the properties of bulk water, despite the apparent simplicity of the molecule, is still a challenge. In order to fully understand and reproduce its complex phase diagram, it is necessary to perform simulations at the level, including quantum mechanical effects both for electrons and nuclei. This comes at a high computational cost, given that the structural and dynamical properties tend to require long timescales and large simulation cells. In this work, we evaluate the errors that density functional theory (DFT)-based simulations routinely incur into due time- and size-scale limitations. These errors are evaluated using neural-network-trained force fields that are accurate at the level of DFT methods. We compare different exchange and correlation potentials for properties of bulk water that require large timescales. We show that structural properties are less dependent on the system size and that dynamical properties such as the diffusion coefficient have a strong dependence on the simulation size and timescale. Our results facilitate comparisons of DFT-based simulation results with experiments and offer a path to discriminate between model and convergence errors in these simulations.
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http://dx.doi.org/10.1021/acs.jpcb.1c04372 | DOI Listing |
Phys Life Rev
January 2025
Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA.
We argue that "processes versus objects" is not a useful dichotomy. There is, instead, substantial theoretical utility in viewing "objects" and "processes" as complementary ways of describing persistence through time, and hence the possibility of observation and manipulation. This way of thinking highlights the role of memory as an essential resource for observation, and makes it clear that "memory" and "time" are also mutually inter-defined, complementary concepts.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
February 2025
Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801.
Enzyme-enzyme interactions are fundamental to the function of cells. Their atomistic mechanisms remain elusive mainly due to limitations of in-cell measurements. We address this challenge by atomistically modeling, for a total of ≈80 μs, a slice of the human cell cytoplasm that includes three successive enzymes along the glycolytic pathway: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), and phosphoglycerate mutase (PGM).
View Article and Find Full Text PDFLangmuir
January 2025
John A. Reif, Jr. Department of Civil and Environmental Engineering, New Jersey Institute of Technology, 323 Martin Luther King Blvd., Newark, New Jersey 07102, United States.
Precise control of nanobubble size is essential for optimizing the efficiency and performance of nanobubble applications across diverse fields, such as agriculture, water treatment, and medicine. Producing fine bubbles, including nanobubbles, is commonly achieved by purging gas through porous media, such as ceramic or polymer membranes. Many operational factors and membrane properties can significantly influence nanobubble production and characteristics.
View Article and Find Full Text PDFAcc Chem Res
January 2025
School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
ConspectusSymmetry is a pervasive phenomenon spanning diverse fields, from art and architecture to mathematics and science. In the scientific realms, symmetry reveals fundamental laws, while symmetry breaking─the collapse of certain symmetry─is the underlying cause of phenomena. Research on symmetry and symmetry breaking consistently provides valuable insights across disciplines, from parity violation in physics to the origin of homochirality in biology.
View Article and Find Full Text PDFJ Chem Phys
January 2025
School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom.
Membrane properties are determined in part by lipid composition, and cholesterol plays a large role in determining these properties. Cellular membranes show a diverse range of cholesterol compositions, the effects of which include alterations to cellular biomechanics, lipid raft formation, membrane fusion, signaling pathways, metabolism, pharmaceutical therapeutic efficacy, and disease onset. In addition, cholesterol plays an important role in non-cellular membranes, with its concentration in the skin lipid matrix being implicated in several skin diseases.
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