相关论文: Medium effects on the selection of sequences foldi…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
The adhesion bonds connecting a lipid bilayer to an underlying surface may undergo a condensation transition resulting from an interplay between a short range attractive potential between them, and a long range fluctuation-induced potential…
We investigate the asymptotic separation of the optical model potential for nucleon-nucleus scattering in momentum space, where the potential is split into a medium-independent term and another depending exclusively on the gradient of the…
The miscibility of polymer blends, a classical problem in polymer science, may be altered, if one or both of the component do not have chain ends. Based on the idea of {\it topological volume}, we propose a mean-field theory to clarify how…
We consider the rupture dynamics of a homopolymer chain pulled at one end at a constant loading rate r. Compared to single bond breaking, the existence of the chain introduces two new aspects into rupture dynamics: the non-Markovian aspect…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Token representations in high-dimensional latent spaces often exhibit redundancy, limiting computational efficiency and reducing structural coherence across model layers. Hierarchical latent space folding introduces a structured…
The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
In two-dimensional rotating drum experiments, we find two separate influences of the packing fraction of a granular heap on its stability. For a fixed grain shape, the stability increases with packing fraction. However, in determining the…
By enumerating all sequences of length 20, we study the designability of structures in a two-dimensional Hydrophobic-Polar (HP) lattice model in a wide range of inter-monomer interaction parameters. We find that although the histogram of…
We consider mediated effects of an exposure, X on an outcome, Y, via a mediator, M, under no unmeasured confounding assumptions in the setting where models for the conditional expectation of the mediator and outcome are partially linear. We…
Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from…
Grain growth competition during solidification determines microstructural features, such as dendritic arm spacings, segregation pattern, and grain texture, which have a key impact on the final mechanical properties. During metal additive…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…