Related papers: Benchmarking inverse statistical approaches for pr…
Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints on each residue site. Selective constraints on residue sites are…
With this contribution, we give a complete and comprehensive framework for modeling the dynamics of complex mechanical structures as port-Hamiltonian systems. This is motivated by research on the potential of lightweight construction using…
A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based…
This paper proposes a new evolutionary algorithm, called DSMGA-II, to efficiently solve optimization problems via exploiting problem substructures. The proposed algorithm adopts pairwise linkage detection and stores the information in the…
In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in…
Singlet fission has emerged as one of the most exciting phenomena known to improve the efficiencies of different types of solar cells and has found uses in diverse optoelectronic applications. The range of available singlet fission…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata…
We present a nonequilibrium strong-coupling approach to inhomogeneous systems of ultracold atoms in optical lattices. We demonstrate its application to the Mott-insulating phase of a two-dimensional Fermi-Hubbard model in the presence of a…
We present a computational scheme for predicting the ligands that bind to a pocket of known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations and…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
Hamiltonian inverse engineering enables the design of protocols for specific quantum evolutions or target state preparation. Perfect state transfer (PST) and remote entanglement generation are notable examples, as they serve as key…
The primitive-path analysis (PPA) {[}R. Everaers et al. Science 303, 823, (2004){]} is an algorithm that transforms a model polymer melt into its topologically equivalent mesh by removing excess contour length stored in thermal…
Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…
As the structural databases continue to expand, efficient methods are required to search similar structures of the query structure from the database. There are many previous works about comparing protein 3D structures and scanning the…
Numerous machine learning (ML) models employed in protein function and structure prediction depend on evolutionary information, which is captured through multiple-sequence alignments (MSA) or position-specific scoring matrices (PSSM) as…