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AlphaFold can be used for both single-chain and multi-chain protein structure prediction, while the latter becomes extremely challenging as the number of chains increases. In this work, by taking each chain as a node and assembly actions as…
The reaction cross section $\sigma_R$ is useful to determine the neutron radius $R_n$ as well as the matter radius $R_m$. The chiral (Kyushu) $g$-matrix folding model for $^{12}$C scattering on $^{9}$Be, $^{12}$C, $^{27}$Al targets was…
Theoretical models of compaction processes, such as for example intergranular pressure-solution (IPS), focus on deformation occurring at the contacts between spherical grains that constitute an aggregate. In order to investigate the…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
Proteins are vital biological molecules found in every living organism, and their function is determined by what shape they fold into. Peptides are essentially subsets of proteins, and therefore ideal as model systems for protein folding.…
Information on the equation of state (EOS) of neutron matter may be gained from studies of 208Pb. Descriptions of 208Pb require credible models of structure, taking particular note also of the spectrum. Such may be tested by analyses of…
Predicting volume swelling of structural materials in nuclear reactors under high-dose neutron irradiations based on existing low-dose experiments or irradiation data with high-dose-rate energetic particles has been a long-standing…
In this paper, we study the accuracy of Irving-Kirkwood type of formulas for the approximation of continuum quantities from atomistic simulations. Such formulas are derived by expressing the displacement, deformation gradient and stress in…
Linear probes are widely used to interpret and evaluate neural representations, yet their reliability remains unclear, as probes may appear accurate in some regimes but collapse unpredictably in others. We uncover a spectral mechanism…
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…
The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
Charges and their contribution to protein-protein interactions are essential for the key structural and dynamic properties of monoclonal antibody (mAb) solutions. In fact, they influence the apparent molecular weight, the static structure…
Understanding and controlling fracture propagation is one of the most challenging engineering problems, especially in the oil and gas sector, groundwater hydrology and geothermal energy applications. Predicting the fracture orientation…
A method previously proposed for calculating the radius of gyration and the intrinsic viscosity of dendrimers is modified to give a more accurate description of existing experimental data. The new method includes some features that were not…
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts…
To describe atomization completely it is necessary to track the liquid-gas interface morphology at any stage of the atomization process. Typically, instability analysis focuses on generic and simplified morphology: cylindrical jet, liquid…
Theories of protein crystallization based on spheres that form close-packed crystals predict optimal assembly within a `slot' of second virial coefficients and enhanced assembly near the metastable liquid-vapor critical point. However, most…
We study swelling and structural properties of ionic microgel suspensions within a comprehensive coarse-grained model that combines the polymeric and colloidal natures of microgels as permeable, compressible, charged spheres governed by…
Proteins experience a wide variety of conformational dynamics that can be crucial for facilitating their diverse functions. How is the intrinsic flexibility required for these motions encoded in their three-dimensional structures? Here, the…