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Elastic scattering is a very important process to understand nuclear interactions in finite nuclei. Despite decades of efforts, the goal of reaching a coherent description of this physical process in terms of microscopic forces is still far…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…
The embedded atom method (EAM) potentials are probably the most widely used interatomic potentials for metals and alloys. However, the EAM potentials impose three constraints on elastic constants that are inconsistent with experiments. At a…
High precision angular distribution data of ($\alpha$,$\alpha$) elastic scattering are presented for the nuclei $^{89}$Y, $^{92}$Mo, $^{106,110,116}$Cd, $^{112,124}$Sn, and $^{144}$Sm at energies around the Coulomb barrier. Such data with…
A previously derived semi-microscopic analysis based on the Double Folding Model, for alpha-particle elastic scattering on A~100 nuclei at energies below 32 MeV, is extended to medium mass A ~ 50-120 nuclei and energies from ~13 to 50 MeV.…
The boundary element method (BEM) enables solving three-dimensional electromagnetic problems using a two-dimensional surface mesh, making it appealing for applications ranging from electrical interconnect analysis to the design of…
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron…
The diffraction slope parameter is investigated for elastic proton-proton and proton-antiproton scattering based on the all available experimental data at low and intermediate momentum transfer values. Energy dependence of the elastic…
Energy-based models (EBMs) provide a powerful and flexible way of learning a joint probability distribution over data by constructing an energy surface. This energy surface enables insight extraction and conditional sampling. We apply EBMs…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
The analyses of elastic collisions of charged nucleons have been based standardly on West and Yennie formula. However, this approach has been shown recently to be inadequate from experimental as well as theoretical points of view. The…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Elastin is a structural protein with outstanding mechanical properties (e.g., elasticity and resilience) and biologically relevant functions (e.g., triggering responses like cell adhesion or chemotaxis). It is formed from its precursor…
Results for elastic electron scattering by nuclei, calculated with charge densities of Skyrme forces and covariant effective Lagrangians that accurately describe nuclear ground states, are compared against experiment in stable isotopes.…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Predicting changes in binding free energy ($\Delta\Delta G$) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between $\Delta\Delta…
A quantum-mechanical model to calculate the electron energy-loss spectra (EELS) for the system of a closely located metallic nanoshell and a molecule has been developed. At the resonance between the molecular excitation and plasmon modes in…
Energy-Based Models (EBMs) have proven to be a highly effective approach for modelling densities on finite-dimensional spaces. Their ability to incorporate domain-specific choices and constraints into the structure of the model through…