Related papers: Ab Initio Nucleic Acid Folding Simulations Using a…
The state-of-the-art ab initio nuclear many-body approaches with modern nuclear forces are challenged by the recent experimental measurement of the monopole form factor of the $0^+_1\rightarrow 0^+_2$ transition in the $\alpha$ particle…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed…
Theoretical modeling of nucleus-nucleus collision often is based on the nucleus-nucleus potential. One of the advanced methods for constructing this potential is the semi-microscopical double-folding model with the M3Y-Paris NN-forces.…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
There has been significant recent progress in solving the long-standing problems of how nuclear shell structure and collective motion emerge from underlying microscopic inter-nucleon interactions. We review a selection of recent significant…
We demonstrate the existence of multiple converging sequences in the ab initio no-core shell model. By examining the underlying theory of effective operators, we expose the physical foundations for the alternative pathways to convergence.…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
AlphaFold 3 represents a transformative advancement in computational biology, enhancing protein structure prediction through novel multi-scale transformer architectures, biologically informed cross-attention mechanisms, and geometry-aware…
The radiation-induced damages in bio-molecules are ubiquitous processes in radiotherapy, radio-biology and critical to space-projects. In this study we present a precise quantification of the fragmentation mechanisms of deoxyribonucleic…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…
Extreme mechanical processes such as strong lattice distortion and bond breakage during fracture are ubiquitous in nature and engineering, which often lead to catastrophic failure of structures. However, understanding the nucleation and…
Carbon dioxide hydrates are ice-like nonstoichiometric inclusion solid compounds with importance to global climate change, and gas transportation and storage. The thermodynamic and kinetic mechanisms that control carbon dioxide nucleation…
This work proposes a new efficient approach for calculating the bending stiffness of two-dimensional materials using simple atomistic tests on small periodic unit cells. The tests are designed such that bending deformations are dominating…
We present a novel theory and implementation for computing coupled electronic and quantal nuclear subsystems on a single potential energy surface, moving beyond the standard Born-Oppenheimer (BO) separation of nuclei and electrons. We…
Here we present the results from two sets of simulations, in two and three spatial dimensions. In two dimensions, the simulations include multifrequency flux-limited diffusion neutrino transport in the "ray-by-ray-plus" approximation,…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
A modified version of the previously proposed exponential model with pairing attenuation for the well deformed even-even nuclei has been applied to predict the energy levels of doubly even actinide nuclei. Satisfactory results are obtained…
The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. However, extracting quantitative models of fundamental…
A feed-forward neural network is demonstrated to efficiently unfold the energy distribution of protons and alpha particles passing through passive material. This model-independent approach works with unbinned data and does not require…