Results 41 to 50 of about 256,961 (259)

Developing a Computational Chemistry Framework for the Exascale Era [PDF]

, 2018
Within computational chemistry, the NWChem package has arguably been the de facto standard for running high-accuracy numerical simulations on the most powerful supercomputers.
de Jong, Wibe, Richard, Ryan M, Richard, Ryan, de Jong, Wibe A., Pritchard, Benjamin, Boschen, Jeffery S., Harrison, Robert, Harrison, Robert J, Valeev, Edward, de Jong, Wibe A, Windus, Theresa L, Windus, Theresa L., Boschen, Jeffery S, Windus, Theresa, Richard, Ryan M., Bertoni, Colleen, Keipert, Kristopher, Valeev, Edward F, Valeev, Edward F., Boschen, Jeffrey, Harrison, Robert J.   +20 more
core   +1 more source

Epigenetic blind spots – the role of DNA methylation dynamics in stem cell‐based models of embryogenesis

FEBS Letters, EarlyView.
Embryo‐like structures (stembryos) are an innovative tool, but they are hindered by experimental variability and limited developmental potential. DNA methylation is crucial for mammalian development, but its status in stembryo models is poorly characterized.
Sara Canil, Anna Corrà, Annalisa Scapolatiello, Chengxiang Qiu, Gianluca Amadei   +4 more
wiley   +1 more source

Structural Characteristics and Reactivity Relationships of Nitroaromatic and Nitramine Explosives – A Review of Our Computational Chemistry and Spectroscopic Research [PDF]

, 2007
Although much has been discovered, discussed and written as to problems ofcontamination by various military unique compounds, particularly by the nitrogen basedenergetics (NOCs), remaining problems dictate further evaluation of actual and potentialrisk ...
Mohammad M. Qasim, Brett Moore, Leonid Gorb, Jerzy Leszczynski, Patricia Honea, Lyssa Taylor   +5 more
core   +1 more source

Massively Scalable Workflows for Quantum Chemistry: BIGCHEM and CHEMCLOUD [PDF]

, 2023
Electronic structure theory, i.e. quantum chemistry, is the fundamental building block for many problems in computational chemistry. We present a new distributed computing framework (BIGCHEM) which allows efficient solution of many quantum chemistry ...
Colton B., Hicks, Todd J., Martinez
core   +1 more source

Modulation of Homer1 EVH1 domain internal dynamics by putative autism‐associated mutations

FEBS Letters, EarlyView.
The putative autism‐associated M65I and S97L variants of the EVH1 domain of the postsynaptic scaffold protein Homer1 do not exhibit substantial changes in their overall structure or partner binding. Both of them, but especially the M65I variant, show altered internal dynamics relative to the wild‐type domain on the μs‐ms timescale, indicated by the ...
Fanni Farkas, Brigitta Maruzs, Zsófia E. Kálmán, Tomas Klumpler, Gyula Batta, Bálint Péterfia, Zoltán Gáspári   +6 more
wiley   +1 more source

Mathematical Optimization in Machine Learning for Computational Chemistry [PDF]

Machine learning (ML) is transforming computational chemistry by accelerating molecular simulations, property prediction, and inverse design. Central to this transformation is mathematical optimization, which underpins nearly every stage of model ...
Zekić, Ana, Ana Zekić
core   +1 more source

Cell geometry and membrane protein crowding constrain Escherichia coli growth rate, overflow metabolism, respiration, and maintenance energy

FEBS Letters, EarlyView.
The physical dimensions and shape of bacterial cells define the surface area available to acquire nutrients and the volume available for synthesizing proteins and DNA. Here, we use computational systems biology to decode the importance of cell geometry as a major determinant of prokaryotic phenotype, including growth rate and metabolic efficiency. This
Ross P. Carlson, Tomáš Gedeon, Mauricio Garcia Benitez, Campbell Putnam, William R. Harcombe, Radhakrishnan Mahadevan, Ashley E. Beck   +6 more
wiley   +1 more source

Comparison of Computational Chemistry Methods for the Discovery of Quinone-Based Electroactive Compounds for Energy Storage [PDF]

, 2020
High-throughput computational screening (HTCS) is an approach that can enable rational and time-efficient discovery of electroactive compounds. The effectiveness of HTCS is dependent on the accuracy and speed at which the performance descriptors can be ...
Abhishek, Khetan, Qi, Zhang, Süleyman, Er   +2 more
core   +1 more source

Modelling stem cell differentiation related processes—A practical overview for biologists

FEBS Letters, EarlyView.
Stem cell differentiation is complex and difficult to control experimentally. This review introduces suitable computational modelling approaches that can support stem cell research, from mechanistic ODE and abstract models to multiscale and deep learning methods.
Ricco Zeegelaar, Xinqi Yan, Lucas F. Jansen Klomp, Stefano Schivo, Janine N. Post   +4 more
wiley   +1 more source

Design and analysis strategies for robust microbiome ageing research

FEBS Letters, EarlyView.
The gut microbiome changes with age and associates with age‐related morbidity and mortality, establishing it as a potential biomarker and intervention target for ageing. Realising this potential requires methodological rigour, yet distinguishing biological signals from methodological artefacts remains challenging across cohorts. This review provides an
Mark Olenik, İsmail Güderer, Yi Wang, Tayyaba Alvi, Prasoon Pandey, Handan Melike Dönertaş   +5 more
wiley   +1 more source